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Changeset 0:b15a3147e604 (2022-03-25)

Next changeset 1:98944ec4bfc7 (2022-03-25)

Commit message:
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

diff -r 000000000000 -r b15a3147e604 test-data/custom_trimmed_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.html Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,74 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.4 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 9 /Selected Residues: 63\n+ Deleted Sequences: 0 /Deleted Residues: 122\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+ Similarity Scores: =0= <1e-6 <1e-5 <1e-4 <.001 <.010 <.100 <.250 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90 100 110 120\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL\n+ Xtr21234 ----MISQVRQNYSHDCEA'..b'span class=nsel> \n+\n+ Gaps Scores: \n+ Similarity Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r b15a3147e604 test-data/custom_trimmed_example.009.AA.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.phy Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,11 @@
+ 9 63
+Csa004271    --------------YMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Xtr21234     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaH         SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Hsa167996    SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Mmu024661    SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Dre37936     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaM         SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Tru14292     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Ola20972     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+

diff -r 000000000000 -r b15a3147e604 test-data/example.004.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.004.AA.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,18 @@
+>Sp8
+FPWNGLQIHMMGIII
+
+>Sp17
+FPWNGLQIHMMGIII
+
+>Sp10
+FPWNGLQIHMMGIII
+
+>Sp26
+FPWNGLQIHMMGIII
+
+>Sp33
+FPWNGLQIHMMGIII
+
+>Sp6
+FPWNGLQIHMMGIII
+

diff -r 000000000000 -r b15a3147e604 test-data/example.009.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.009.AA.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,45 @@
+>Csa004271
+---------------------------------MYMAMGHFFDRDDVALKNISEYFKECS
+EEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL
+HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS
+-----
+>Xtr21234
+----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQS
+KEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL
+HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS-
+-----
+>LcaH
+----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQS
+HEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL
+HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGK
+ES--S
+>Hsa167996
+MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL
+HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGD
+SDNES
+>Mmu024661
+MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL
+HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGH
+GD-ES
+>Dre37936
+---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNS
+EEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL
+HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS
+-----
+>LcaM
+----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENS
+DEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL
+HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGG
+KS---
+>Tru14292
+----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENS
+DEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL
+HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGS
+KS---
+>Ola20972
+----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENS
+HEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL
+HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGS
+KS---
\ No newline at end of file

diff -r 000000000000 -r b15a3147e604 test-data/trimmed_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_example.009.AA.html Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,71 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.4 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 9 /Selected Residues: 174\n+ Deleted Sequences: 0 /Deleted Residues: 11\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90 100 110 120\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL\n+ Xtr21234 ----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYF<spa'..b'd=m>DFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS---\n+\n+ Selected Cols: \n+\n+ Gaps Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r b15a3147e604 test-data/trimmed_example.009.AA.mega
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_example.009.AA.mega Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,58 @@
+#MEGA
+!Title ./test-data/example.009.AA.fasta;
+!Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard;
+
+#Csa004271
+---------- ---------- ---------M YMAMGHFFDR DDVALKNISE
+YFKECSEEER EHANKMIEFH NKRGGTTTYF PIKAPGSFDP ANTIKAMNCA
+LALEVNVNKS LLALHE--TA NGDPEFQDFI EANFLHEQVD AIKKLKDYIT
+NLKLVG---T GLGEFLFDKH FKSS
+
+#Xtr21234
+MISQVRQNYS HDCEAAVNRM VNLEMYASYT YLSMSHYFDR DDVALHHVAE
+FFKEQSKEER ECAEKLMKCQ NKRGGRIVLQ DIKKPERDEW GSTLDAMQTA
+LDLEKHVNQA LLDLHNLATE RKDPHICDFL ESEHLDEQVK HMKKFGDHIT
+NLKRLGVPQN GMGEYLFDKH SLS-
+
+#LcaH
+MSSQVRQNFH QDCEAAINRQ INLELYASYV YLSMAYYFDR DDQALHNFAK
+FFRHQSHEER EHAEKLMKLQ NQRGGRIFLQ DVRKPDRDEW GSGVEALECA
+LQLEKSVNQS LLDLHKLCSD HNDPHLCDFI ETHYLDEQVK SIKELADWVT
+NLRRMGAPQN GMAEYLFDKH TLGK
+
+#Hsa167996
+STSQVRQNYH QDSEAAINRQ INLELYASYV YLSMSYYFDR DDVALKNFAK
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDCDDW ESGLNAMECA
+LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT
+NLRKMGAPES GLAEYLFDKH TLGD
+
+#Mmu024661
+SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDDW ESGLNAMECA
+LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT
+NLRKMGAPEA GMAEYLFDKH TLGH
+
+#Dre37936
+ETSQIRQNYV RDCEAAINKM INLELYAGYT YTSMAHYFKR DDVALPGFAK
+FFKKNSEEER EHAEKFMEFQ NKRGGRIVLQ DIKKPDRDVW GNGLIAMQCA
+LQLEKNVNQA LLDLHKLATE MGDPHLCDFL ETHYLNEQVE AIKKLGDHIT
+NLSKMDAGNN RMAEYLFDKH TLDS
+
+#LcaM
+MESQVRQNYH RDCEAAVNRM VNMEMFASYT YTSMAFYFSR DDVALPGFSH
+FFKENSDEER EHAEKLLSFQ NKRGGHIFLQ DIKKPERDEW GSGLEAMQCA
+LQLKKNVNQA LLDLHKLASD HGDPHLCDFL ETHYLNEQVE AIKKLGDYIS
+NLSRMDAQKN KMAEYLFDKH SLGG
+
+#Tru14292
+MESQVRQNYH RDCEAAINKM INMELYASYT YTSMAFFFSR DDVALPGFAH
+FFKENSDEER EHAEKLLSFQ NKRGGRIFLQ DIKKPERDEW GSGLEAMQCA
+LQLEKKVNQA LLDLHKLASD HVDPHLCDFL ESHYLNEQVE AIKKLGDYIT
+NLSRMDAQNN KMAEYLFDKH TLGS
+
+#Ola20972
+MESQVRQNYH RDCEAAINRM VNMELFASYT YTSMAFYFDR DDVALPGFSH
+FFKENSHEEK EHADKLLSFQ NKRGGRIFLQ DVKKPERDEW GSGLEAMQCA
+LQLEKNVNQA LLDLHKVASD HKDPHMCDFL ETHYLNEQVE SIKKIGDHIT
+NLTRMDAHTN KMAEYLFDKH TLGS
+

diff -r 000000000000 -r b15a3147e604 trimal.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal.xml Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,123 @@
+<tool id="trimal" name="trimAl: a tool for automated alignment trimming" version="0.1.0" python_template_version="3.5">
+ <requirements>
+ <requirement type="package" version="1.4.1">trimal</requirement>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[
+ trimal -in $input1 -out $trimmed_output -htmlout $html_summary ${out_format_selector}
+ #if $trimming_mode.mode_selector == "custom"
+ -gapthreshold $trimming_mode.gapthreshold
+ -simthreshold $trimming_mode.simthreshold
+ -cons $trimming_mode.cons
+ #else:
+ $trimming_mode.mode_selector
+ #end if
+ ;
+
+ ]]></command>
+ <inputs>
+ <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" />
+ <conditional name="trimming_mode">
+ <param name="mode_selector" type="select" label="Select trimming mode from the list">
+ <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option>
+ <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option>
+ <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option>
+ <option value="-strict">strict. (see User Guide)</option>
+ <option value="-strictplus">strictplus. (see User Guide)</option>
+ <option value="custom">Custom mode</option>
+ </param>
+ <when value="custom">
+ <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gap threshold" help="1 - (fraction of sequences with a gap allowed). Range: [0 - 1]" multiple="false"/>
+ <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/>
+ <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="min conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve." multiple="false"/>
+
+ </when>
+ </conditional>
+ <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
+ <option value="-clustal">CLUSTAL format</option>
+ <option value="-fasta">FASTA format</option>
+ <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option>
+ <option value="-nbrf">NBRF/PIR format</option>
+ <option value="-nexus">NEXUS format</option>
+ <option value="-mega">MEGA format</option>
+ <option value="-phylip">PHYLIP/PHYLIP4 format</option>
+ <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option>
+ <option value="-phylip_paml">PHYLIP format compatible with PAML</option>
+ <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option>
+ <option value="-phylip3.2">PHYLIP3.2 format</option>
+ <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option>
+ </param>
+ </inputs>
+ <outputs>
+ <data name="trimmed_output" format="fasta" label="Trimmed alignment."/>
+ <data name="html_summary" format="html" label="trimal html summary."/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="input1" value="example.009.AA.fasta"/>
+ <param name="mode_selector" value="-gappyout" />
+ <param name="out_format_selector" value="-mega" />
+ <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/>
+ <output name="html_summary" file="trimmed_example.009.AA.html"/>
+ </test>
+ <test>
+ <param name="input1" value="example.009.AA.fasta"/>
+ <param name="mode_selector" value="custom" />
+ <param name="gapthreshold" value="0.5" />
+ <param name="simthreshold" value="0.5" />
+ <param name="cons" value="5" />
+ <param name="out_format_selector" value="-phylip_paml_m10" />
+ <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" />
+ <output name="html_summary" file="custom_trimmed_example.009.AA.html"/>
+ </test>
+ </tests>
+ <help><![CDATA[
+Modes
+ -nogaps Remove all positions with gaps in the alignment.
+ -noallgaps Remove columns composed only by gaps.
+ -gappyout Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
+ -strict Use automatic selection on "strict" mode. (see User Guide).
+ -strictplus Use automatic selection on "strictplus" mode. (see User Guide).
+ trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón.
+
+Custom mode parameters
+ -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed).
+ -st -simthreshold <n> Minimum average similarity allowed.
+ -cons <n> Minimum percentage of the positions in the original alignment to conserve.
+
+Output formats
+ -nbrf Output file in NBRF/PIR format
+ -mega Output file in MEGA format
+ -nexus Output file in NEXUS format
+ -clustal Output file in CLUSTAL format
+ -fasta Output file in FASTA format
+ -fasta_m10 Output file in FASTA format. Sequences name length up to 10 characters.
+ -phylip Output file in PHYLIP/PHYLIP4 format
+ -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters.
+ -phylip_paml Output file in PHYLIP format compatible with PAML
+ -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name length up to 10 characters.
+ -phylip3.2 Output file in PHYLIP3.2 format
+ -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name length up to 10 characters.
+
+trimAl webpage: http://trimal.cgenomics.org
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, the last available version.
+
+Please cite:
+ trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
+ Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
+ Bioinformatics 2009, 25:1972-1973.
+ ]]></help>
+ <citations>
+ <citation type="bibtex">
+@misc{githubTrimAl,
+ author = {LastTODO, FirstTODO},
+ year = {TODO},
+ title = {TrimAl},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/inab/trimal},
+}</citation>
+ </citations>
+</tool>
\ No newline at end of file

diff -r 000000000000 -r b15a3147e604 trimal_repo/AUTHORS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/AUTHORS Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,16 @@
+** Authors **
+
+Salvador Capella-Gutierrez.
+  Comparative Genomics Group. Bioinformatics and Genomics Department.
+  Centre for Genomic Regulation. Barcelona, Spain.
+  e-mail: scapella _at_ crg.es
+
+Toni Gabaldón.
+  Comparative Genomics Group. Bioinformatics and Genomics Department.
+  Centre for Genomic Regulation. Barcelona, Spain.
+  e-mail: tgabaldon _at_ crg.es
+
+** Authors (until trimAl v1.1) **
+
+Jose Ma. Silla-Martínez.
+  e-mail: josilma1 _at_ gmail.com

diff -r 000000000000 -r b15a3147e604 trimal_repo/CHANGELOG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/CHANGELOG Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,150 @@
+trimAl/readAl v1.3. April 2011.
+
+[General]
+
+  * Rewritten all file format parsers.
+
+  * Added a new file format for compatibility with some programs.
+    * phylip_paml
+
+  * Extended some file format parsers.
+    * fasta_m10
+    * phylip_m10
+    * phylip3.2_m10
+    * phylip_paml_m10
+
+  * A new control versions system is used: git.
+
+  * Improved general system for tracking builds/revisions.
+
+  * Refactored some portion of codes for improving its legibility and
+    comprehension.
+
+[trimAl]
+
+  * Improved HTML functionality. Now trimAl's summary shows which scores have been used
+    for trimming the alignment along with scores scales bars.
+
+  * Now it is possible to get an HTML trimAl's summary of previously no-allowed combinations
+    of trimming methods. No-allowed combinations were related to the use of methods based on
+    several alignments (consistency based scores) and methods based on a single alignment.
+
+  * Some previously no allowed combinations between different trimming methods now are permitted.
+    This is oriented to trim a given alignment using scores from several alignments along with
+    scores computed from a single alignment.
+
+  * When several alignment are given now it is possible to force the selection of one
+    of them using a new option "-forceselect". This is useful to trim a specific alignment
+    based on its consistency scores computed from a given set of alignments independently
+    if that alignment is the most consistent among the set of those alignments.
+    The selected alignment should not be present among alignments in the "-compareset"
+    input file.
+
+  * Former "-select" option has been converted into "-selectcols" for removing specific
+    columns/range of columns.
+
+  * Added the possibility, using "-selectseqs" option, to remove specific sequences/range
+    of sequences from input alignment.
+
+  * Using "-backtrans" option it is possible to trim an input protein alignment and then
+    get a back-translated CDS alignment. Coding DNA sequences are mapped before trimming
+    to protein sequences through sequences identifiers controlling stop codons, sequences
+    lengths, etc, etc.
+
+  * Using "-splitbystopcodon" option is possible, when a back-translation is done, to split
+    input coding sequences for its stop codons (at positions multiple of 3).
+
+  * Added a new option "-terminalonly" for removing only columns out of internal boundaries.
+    Internal boundaries are defined as the first and last column in the alignment without
+    gaps. The columns removal depends on the applied trimming method, that means, if there
+    is not columns to be deleted out of internal boundaries, no-columns will be deleted.
+    All columns in-between internal boundaries are kept independently of any trimming methods
+    decision.
+
+  * Added a new option "-clusters" for getting the most Nth representative sequences from
+    input alignment. Representativeness is computed in terms of identity between each pair
+    of sequences in the alignment. Then an algorithm is applied for constructing a set of
+    clusters based on those identities values. The longest sequences is selected as the
+    cluster representative for the final alignment.
+
+  * Added a new option "-maxidentity" for getting sequences representatives at given identity
+    threshold. This option allows to get the set of sequences/cluster representatives with an
+    identity below to that threshold regarding to rest of the sequences. Sequences with identities
+    scores higher than established threshold are clusters to the most similar sequence. The
+    longest sequences are selected as cluster representatives for the final alignment.
+
+  * Added a new option "-block" for keeping only columns blocks equal or higher to that size
+    in the final alignment. This option is available for manual trimming methods and only for
+    "gappyout" method among automated ones.
+
+  * Changed identity scores matrix. Now it is shown "100.000" in the diagonal instead of
+    "0". It makes more sense to have a score of 100 for each sequence against itself.
+
+  * Changed options name for making clear their meaning.
+    * scc => ssc  - Similarity scores for columns in the alignment.
+    * sct => sst  - Cumulative distribution of similarities scores in the alignment.
+
+[readAl]
+
+  * Added new option "-reverse" for getting the reverse of the input alignment.
+
+  * Added new option "-onlyseqs" for getting only sequences from the alignment. This option
+    destroys input alignment and returns a fasta file with unaligned sequences.
+
+  * Added new option "-html" for getting an HTML file with alignments residues colored
+    according to CLUSTAL scheme. This functionality is similar to SeaView/JalView visualization.
+
+  * Changed option "-format". Now it informs about input file format and if sequences are
+    aligned or not.
+
+  * Updated option "-type". Now it informs more about nucleotides datatype: dna or rna.
+
+trimAl/readAl v1.2. April 2009.
+
+  * Added the htmlout to track the trimAl's trimming.
+
+  * Added the possibility to delete spurious sequences from the alignment.
+
+  * Added the complementary and colnumbering options.
+
+  * Added the manual selection of columns.
+
+  * Added one new heuristic method to select the best automated trimming method.
+    * Automated1
+
+  * Added two new automated methods to work with gaps and similarity distribution.
+    * Strict
+    * Strictplus
+
+  * Select only one automated method to work with gaps distribution.
+    * Strict => Gappyout
+    * Relaxed was deleted
+
+  * Added the version/revisions system.
+
+  * Improved the file format.
+    * Added support for phylip 3.2
+    * Added support for clustal
+    * Added support for fasta
+    * Added support for nexus
+    * Added support for mega
+    * Added support for nbrf/pir
+
+  * Improved of statistics methods.
+    * Improved the information of the available methods.
+    * Added the identity statistics.
+
+  * Improved of windows size methods.
+    * Consistency windows size.
+
+  * Improved the similarity-matrices handling.
+
+  * Improved the support for DNA/RNA alignments.
+
+  * Added readAl.
+
+  * Fixed some bugs from the previous version.
+
+trimAl v1.1. February 2008.
+
+  * Initial public version of trimAl.

diff -r 000000000000 -r b15a3147e604 trimal_repo/LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/LICENSE Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,674 @@\n+ GNU GENERAL PUBLIC LICENSE\n+ Version 3, 29 June 2007\n+\n+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+ Preamble\n+\n+ The GNU General Public License is a free, copyleft license for\n+software and other kinds of works.\n+\n+ The licenses for most software and other practical works are designed\n+to take away your freedom to share and change the works. By contrast,\n+the GNU General Public License is intended to guarantee your freedom to\n+share and change all versions of a program--to make sure it remains free\n+software for all its users. We, the Free Software Foundation, use the\n+GNU General Public License for most of our software; it applies also to\n+any other work released this way by its authors. You can apply it to\n+your programs, too.\n+\n+ When we speak of free software, we are referring to freedom, not\n+price. Our General Public Licenses are designed to make sure that you\n+have the freedom to distribute copies of free software (and charge for\n+them if you wish), that you receive source code or can get it if you\n+want it, that you can change the software or use pieces of it in new\n+free programs, and that you know you can do these things.\n+\n+ To protect your rights, we need to prevent others from denying you\n+these rights or asking you to surrender the rights. Therefore, you have\n+certain responsibilities if you distribute copies of the software, or if\n+you modify it: responsibilities to respect the freedom of others.\n+\n+ For example, if you distribute copies of such a program, whether\n+gratis or for a fee, you must pass on to the recipients the same\n+freedoms that you received. You must make sure that they, too, receive\n+or can get the source code. And you must show them these terms so they\n+know their rights.\n+\n+ Developers that use the GNU GPL protect your rights with two steps:\n+(1) assert copyright on the software, and (2) offer you this License\n+giving you legal permission to copy, distribute and/or modify it.\n+\n+ For the developers\' and authors\' protection, the GPL clearly explains\n+that there is no warranty for this free software. For both users\' and\n+authors\' sake, the GPL requires that modified versions be marked as\n+changed, so that their problems will not be attributed erroneously to\n+authors of previous versions.\n+\n+ Some devices are designed to deny users access to install or run\n+modified versions of the software inside them, although the manufacturer\n+can do so. This is fundamentally incompatible with the aim of\n+protecting users\' freedom to change the software. The systematic\n+pattern of such abuse occurs in the area of products for individuals to\n+use, which is precisely where it is most unacceptable. Therefore, we\n+have designed this version of the GPL to prohibit the practice for those\n+products. If such problems arise substantially in other domains, we\n+stand ready to extend this provision to those domains in future versions\n+of the GPL, as needed to protect the freedom of users.\n+\n+ Finally, every program is threatened constantly by software patents.\n+States should not allow patents to restrict development and use of\n+software on general-purpose computers, but in those that do, we wish to\n+avoid the special danger that patents applied to a free program could\n+make it effectively proprietary. To prevent this, the GPL assures that\n+patents cannot be used to render the program non-free.\n+\n+ The precise terms and conditions for copying, distribution and\n+modification follow.\n+\n+ TERMS AND CONDITIONS\n+\n+ 0. Definitions.\n+\n+ "This License" refers to version 3 of the GNU General Public License.\n+\n+ "Copyright" also means copyright-like laws that apply to other kinds of\n+works, such as semiconductor masks.\n+\n+ "The Program" refers to a'..b'THE PROGRAM\n+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\n+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n+\n+ 16. Limitation of Liability.\n+\n+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS\n+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY\n+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE\n+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF\n+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD\n+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),\n+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF\n+SUCH DAMAGES.\n+\n+ 17. Interpretation of Sections 15 and 16.\n+\n+ If the disclaimer of warranty and limitation of liability provided\n+above cannot be given local legal effect according to their terms,\n+reviewing courts shall apply local law that most closely approximates\n+an absolute waiver of all civil liability in connection with the\n+Program, unless a warranty or assumption of liability accompanies a\n+copy of the Program in return for a fee.\n+\n+ END OF TERMS AND CONDITIONS\n+\n+ How to Apply These Terms to Your New Programs\n+\n+ If you develop a new program, and you want it to be of the greatest\n+possible use to the public, the best way to achieve this is to make it\n+free software which everyone can redistribute and change under these terms.\n+\n+ To do so, attach the following notices to the program. It is safest\n+to attach them to the start of each source file to most effectively\n+state the exclusion of warranty; and each file should have at least\n+the "copyright" line and a pointer to where the full notice is found.\n+\n+ <one line to give the program\'s name and a brief idea of what it does.>\n+ Copyright (C) <year> <name of author>\n+\n+ This program is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, either version 3 of the License, or\n+ (at your option) any later version.\n+\n+ This program is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with this program. If not, see <http://www.gnu.org/licenses/>.\n+\n+Also add information on how to contact you by electronic and paper mail.\n+\n+ If the program does terminal interaction, make it output a short\n+notice like this when it starts in an interactive mode:\n+\n+ <program> Copyright (C) <year> <name of author>\n+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w\'.\n+ This is free software, and you are welcome to redistribute it\n+ under certain conditions; type `show c\' for details.\n+\n+The hypothetical commands `show w\' and `show c\' should show the appropriate\n+parts of the General Public License. Of course, your program\'s commands\n+might be different; for a GUI interface, you would use an "about box".\n+\n+ You should also get your employer (if you work as a programmer) or school,\n+if any, to sign a "copyright disclaimer" for the program, if necessary.\n+For more information on this, and how to apply and follow the GNU GPL, see\n+<http://www.gnu.org/licenses/>.\n+\n+ The GNU General Public License does not permit incorporating your program\n+into proprietary programs. If your program is a subroutine library, you\n+may consider it more useful to permit linking proprietary applications with\n+the library. If this is what you want to do, use the GNU Lesser General\n+Public License instead of this License. But first, please read\n+<http://www.gnu.org/philosophy/why-not-lgpl.html>.\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/README Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,16 @@
+Basic Installation
+==================
+
+The simplest way to compile this package is:
+
+  1. 'cd' to the directory containing the package's source code ('source').
+
+  2. Type 'make' to compile the package.
+
+  3. Optionally, run trimAl/readAl with the examples into the 'dataset'
+     directory to check the correct installation.
+
+   By default, 'make' compiles the source code of trimAl and readAl in the
+current directory. After that, you can either add to PATH the current
+directory or move these files to '/usr/local/bin' or to '/usr/bin' using
+root privileges.

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/alignments_comparison.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/alignments_comparison.1 Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,3 @@
+../dataset/example.001.AA.phy
+../dataset/example.001.AA.msl
+../dataset/example.001.AA.clw

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/alignments_comparison.2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/alignments_comparison.2 Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,3 @@
+../dataset/example.011.AA.YKL197C.clw
+../dataset/example.011.AA.YKL197C.fasta
+../dataset/example.011.AA.YKL197C.phy

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/alignments_comparison.3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/alignments_comparison.3 Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,2 @@
+../dataset/example.012.AA.SuperAlignment.phy
+../dataset/example.013.AA.SuperAlignment.phy

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.001.AA.clw
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.001.AA.clw Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,10 @@
+CLUSTAL 2.0.12 multiple sequence alignment
+
+
+Sp8             -----GLGKVIV-YGIVLGTKSDQFSNWVVWLFPWNGLQIHMMGII
+Sp10            -------DPAVL-FVIMLGTIT-KFS--SEWFFAWLGLEINMMVII
+Sp26            AAAAAAAAALLTYLGLFLGTDYENFA--AAAANAWLGLEINMMAQI
+Sp6             -----ASGAILT-LGIYLFTLCAVIS--VSWYLAWLGLEINMMAII
+Sp17            --FAYTAPDLL-LIGFLLKTVA-TFG--DTWFQLWQGLDLNKMPVF
+Sp33            -------PTILNIAGLHMETDI-NFS--LAWFQAWGGLEINKQAIL
+                          :    : : *    :.        * **:::    :

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.001.AA.msl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.001.AA.msl Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,9 @@
+ 6 46
+Sp8          -----GLGKVIV-YGIVLGTKSDQFSNWVVWLFPWNGLQIHMMGII
+Sp17         --FAYTAPDLLL-IGFLLKTV-ATFG--DTWFQLWQGLDLNKMPVF
+Sp10         ------DPAVL--FVIMLGTI-TKFS--SEWFFAWLGLEINMMVII
+Sp26         AAAAAAAAALLTYLGLFLGTDYENFA--AAAANAWLGLEINMMAQI
+Sp33         -------PTILNIAGLHMETD-INFS--LAWFQAWGGLEINKQAIL
+Sp6          -----ASGAILT-LGIYLFTLCAVIS--VSWYLAWLGLEINMMAII
+
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.001.AA.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.001.AA.phy Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,9 @@
+ 6 60
+Sp8          ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII
+Sp17         --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF
+Sp10         ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII
+Sp26         AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI
+Sp33         -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL
+Sp6          ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII
+
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.002.AA.clw
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.002.AA.clw Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,9 @@
+ 6 42
+Sp8          ---GLGKVIV-YGIVLGTKSDQFSVVWLFPWNGLQIHMMGII
+Sp17         FAYTAPDLL-LIGFLLKTVA-TFGDTWFQLWQGLDLNKMPVF
+Sp10         -----DPAVL-FVIMLGTIT-KFSSEWFFAWLGLEINMMVII
+Sp26         AAAAAAALLTYLGLFLGTDYENFAAAAANAWLGLEINMMAQI
+Sp33         -----PTILNIAGLHMETDI-NFSLAWFQAWGGLEINKQAIL
+Sp6          ---ASGAILT-LGIYLFTLCAVISVSWYLAWLGLEINMMAII
+
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.002.AA.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.002.AA.phy Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,8 @@
+ 6 60
+Sp17         --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF
+Sp10         ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII
+Sp8          ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII
+Sp33         -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL
+Sp6          ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII
+Sp26         AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.003.AA.clw
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.003.AA.clw Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,8 @@
+ 6 42
+Sp6          ---ASGAILT-LGIYLFTLCAVISVSWYLAWLGLEINMMAII
+Sp17         FAYTAPDLL-LIGFLLKTVA-TFGDTWFQLWQGLDLNKMPVF
+Sp10         -----DPAVL-FVIMLGTIT-KFSSEWFFAWLGLEINMMVII
+Sp8          ---GLGKVIV-YGIVLGTKSDQFSVVWLFPWNGLQIHMMGII
+Sp26         AAAAAAALLTYLGLFLGTDYENFAAAAANAWLGLEINMMAQI
+Sp33         -----PTILNIAGLHMETDI-NFSLAWFQAWGGLEINKQAIL
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.004.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.004.AA.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,18 @@
+>Sp8
+FPWNGLQIHMMGIII
+
+>Sp17
+FPWNGLQIHMMGIII
+
+>Sp10
+FPWNGLQIHMMGIII
+
+>Sp26
+FPWNGLQIHMMGIII
+
+>Sp33
+FPWNGLQIHMMGIII
+
+>Sp6
+FPWNGLQIHMMGIII
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.005.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.005.AA.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,24 @@
+>Sp8
+FPWNGLQIHMMGIII---------------------------------------------
+------------------------------
+
+>Sp17
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------
+------------------------------
+
+>Sp10
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+------------------------------
+
+>Sp26
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+------------------------------
+
+>Sp33
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIII---------------
+
+>Sp6
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.006.AA.pir
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.006.AA.pir Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,62 @@
+>P1;CRAB_ANAPL
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
+  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
+  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
+  SDVPERSIPI TREEKPAIAG AQRK-----*
+
+>P1;CRAB_BOVIN
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR
+  PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
+  QASGPERTIP ITREEKPAVT AAPK----K*
+
+>P1;CRAB_CHICK
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDITIHNPLV RRPLFSWLTP SRIFDQIFGE HLQESELLPT SPSLSPFLMR
+  SPFFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMIEIH
+  GKHEERQDEH GFIAREFSRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
+  SDVPERSIPI TREEKPAIAG SQ-----RK*
+
+>P1;CRAB_HUMAN
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN) (ROSENTHAL FIBER).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPT STSLSPFYLR
+  PPSFLRAPSW FDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK
+  QVSGPERTIP ITREEKPAVT AAPK--K--*
+
+>P1;CRAB_MESAU
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFST ATSLSPFYLR
+  PPSFLRAPSW IDTGLSEMRM EKDRFSVNLD VKHFSPEELK VKVLGDVVEV
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK
+  QASGPERTIP ITREEKPAVT AAPKKKKKK*
+
+>P1;CRAB_MOUSE
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN) (P23).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFST ATSLSPFYLR
+  PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
+  QVSGPERTIP ITREEKPAVA AAPKK----*
+
+>P1;CRAB_RABIT
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPT STSLSPFYLR
+  PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK
+  QAPGPERTIP ITREEKPAVT AAPKK----*
+
+>P1;CRAB_RAT
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFST ATSLSPFYLR
+  PPSFLRAPSW IDTGLSEMRM EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK
+  QASGPERTIP ITREEKPAVT AAP----KK*
+
+>P1;CRAB_SQUAC
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDIAIQHPWL RRPLFPSSIF PSRIFDQNFG EHFDPDLFPS FSSMLSPFYW
+  RMGAPMARMP SWAQTGLSEL RLDKDKFAIH LDVKHFTPEE LRVKILGDFI
+  EVQAQHEERQ DEHGYVSREF HRKYKVPAGV DPLVITCSLS ADGVLTITGP
+  RKVADVPERS VPISRDEKPA VAGPQQKKK*

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.007.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.007.AA.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,528 @@\n+>Mlp\n+----------------------------------------------------MITPFINQ\n+LHSKLSLLSDHPNVKHSSQDKIKPSSIHPFLSGNFAPVH-IEHSLTLCQF-SGGLPDELV\n+GGQYLRNGANPLHL-----PTPDQPYHWFDGDGMIHGVYF--------SSSSAPLYVNRF\n+VDTDIYRASKRRGN---SILPSIASLISPISSPASLLATILRAVFINWL-----------\n+SNVSRLTVANTALVFHDRRLLATCESGPTVAIHAPQLDTIDYHVFPDEATGK-NGLG---\n+QAPLVVGAESTAAGHPIGGMLEEWTSGHPKVDPINGELVFIGCNIFARPFVTHSVVSHTG\n+HHVS------------FKKPIHDVIQPKMMHDFGASHGHTVILDLPLTMDPINLLKPGAP\n+PIVHFDRTLSSRFGVLPRYDPTATRWFTA-SPCLILHTANTWDSTRSSTLRDLGLRSKES\n+EHENYVAVNMLACRFRTAKLVYTAGDLEPPLAEQ--------------------------\n+-----------------------------------TDQDIVRLTYYRFSLSEDDPL-WSG\n+PDSITQPSHLFALSAIPFEFPVLPPNKLMSEVQWVYGCSMA--SGSFDAGLRGGARPNVL\n+VKMNVRELIKRGIKSVKSGKTGPKDQDGIFEVDSRTMPDLL---------------KSEP\n+DSSIRLLELPKGFYLQEPSFIPRKEATR---------EDQGWLVCYVFDENQ-L-EENGQ\n+ASLKAYSELWVLDAELIGEGRSWEEVLVCRVRLPSRVPYGLHSTFLNSEEIQNQRSNSRS\n+NVRLHEHEKN---------------------GKVVLASRFQEGLVWVFGGEDELEDL---\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------\n+>Uma\n+MVKGSSNRRQHSASLQGLPSSQHCAPVISIPSPPPPAEDHAYPPSSFTIPLSKDEELAEA\n+GPSRPGSSAISRRPVLSRRRTSKKEYVHPYLSGNFAPVT-TECPLTDCLF-EGTIPEEFA\n+GSQYVRNGGNPLAN-----SERDRDAHWFDADGMLAGVLF----RRTPKGTIQPCFLNRF\n+ILTDLLLSTPEHSRL--PYVPSIATLVNPHTSVFWLLCEIIRTFVLAMLTWLPGLGLGGN\n+QKLKRISVANTSVFWHDGKAMAGCESGPPMRIMLPGLETAGWYTGEEDKEKE-TCDKNSG\n+NSLTSSSSKGFGGGPPIVSMLREFTTAHPKIDPRTQELLLYHMC-FEPPYLRISVIPASQ\n+SKKT---DLPAHAKTIKGKAVRGLKQPKMMHDFGATATQTVIIDVPLSLDMMNLVR--GK\n+PILHYDPSQPTRFGILPRYEPERVRWYESAEACCIYHTANSWDDDGKFDASHEH-----A\n+TRSAIRGVNMLGCRLNSATLVYSAGNLLPPSHVL--------------------------\n+--------------------------------PPPNCPEKCQLYYWRF------DL---E\n+HAETNTISHEFALSDIPFEFPTINEDYSMQQACYVYGTSMR--DGTFDAGLGKAAKIDAL\n+VKLDAQALIRKGKAMWSQGRLKAGD-----SVDTRTVEEVLTAQRDG---------SASP\n+EDPIKIFEMPRGWYAQETTFVPRRSSTN-----ETSQEDDGWLVCYVFDEATGLHPSTGE\n+VLPGASSELWIIDAKLMSR-------VVCRIKLPQRVPYGLHGTLFTEEQIASQKPIDPS\n+QVRSWALSINLADPFSSSALGSTVYSAAGKAATSKFKNREETYAAFIKDPIRIGAWWVKR\n+NIELLIA-----------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------\n+>Rgr\n+------------------------------------------------------------\n+----------MGARPH------------PFREGNYAPVR-DERQLEPCTC-EGELPLELA\n+GGMYVRNGGEPALAESMR-DDAAPAYHWFDGDGMLTGVYFQEARTATGRRHLVPTFVNRY\n+VLTDVYLAS-HALGLKTPILPSIATLVGSIWTLPLILLAIFRAVFLAFLSFFTH------\n+SPLRHLSVANTSILWHDGRALASCESGPLTWVTLPALDTVGYWSL-EGDDGE-PGLR---\n+--------------EGMIGWMKEWTTAHPKRDPTTGELMLFHMT-FLPPYLHYSVIPSTP\n+AASE----KAEPTPRILAAPVP-ISSPKMMHDMAASREHSILLDLPLSLNPLNLAV--GK\n+PMIHYDPAQRSRFGVLPRHAPDLVRWFEA-PPCIIFHTAFAADVYDPH------------\n+DSTRVDAVELVCCRLNSPRLVYAAGNLDLPVAQA--------------------------\n+--------------------------------LPAGAKEACELYYYSF------SM---S\n+SPTATSPSHAFPLSSIPFEFPTVPQARVVGPAKYVYGCSIK--HGNFDAALGGAAKIDCL\n+VKVNVDALVRRGHK-----RAEAGKGDSERPVDERTVSEVLAQQTSRT--------SNDD\n+DVPIRILQMPPRHYAQESSFVPRANPRS---------EDDGYLLTYVFDEHQ-LDEATGQ\n+PRDGATSELWVVDAWDLET-------VVAKVKLPQRVPYGLHGNWFTADEIREQRDVASV\n+RSRP--------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+----------------------------'..b'GRDAHWFDGDGMLSGVAF--GRISPNDGRIIPKFVNQF\n+ILTDLYLSK-KTTAVSSPIMPSITTLVNPLSTLFQIILSVLRTVFLVFLSHLPASQ----\n+QAIKRISVANTSILYHDGRALATCESGPPMRIQLPSLDTVGWFDG-VQAEGE-PEGV---\n+--ESQLDARRF-GGNGALSFLKEWTTGHPKVDDRTGEMLLYHNT-FVPPFVHYSVIPSSL\n+SNNS-----NTPKLKLINEPVAGVSGARMMHDFGASHTQTIIMDLPLSLDPLNLLR--NR\n+EVVSYDSSKPSRFGVFPRHKPDDVRWFTS-PACCIFHTANAWDTIV--------------\n+-ERKVASVNLLACRMTSATLIYSAGNIAPPNVLS----------NTENIELEETRSIKEN\n+LHGPLGTMCHYEKGPVLESSTSTPNAPNCPSAHASEDNDQCRLYYYEF------DL---S\n+TTGKNQVSHEWALSAIPFEFPSVRPDCEMQQARYIYGCTTS--SSCFGVALGKAVKINVI\n+AKIDSKRLIQKGKD----MHITPVKG----CVDERTVREIID--------------EDNK\n+DDPIQCFRLPTNHFAQEPRFIPRSSSDE---------EDGGYLLFYVFDESQ-L-NLSGE\n+CPTSAVSELWILDAKSMRN-------VIARITLPQRVPYGLHGTWFSHSDIEKQRDVKTF\n+RSLEQLQTK----------------------KQKWESDRKQWWCSWVQWGDMLEKAVG--\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------\n+>Gfu\n+----------------------------------------------------------MK\n+FLQQNSFTQTSMSQPH---EDVSPAIRHPYLTGNFAPIH-KTTNLTPCTY-SGCIPPELT\n+GGQYVRNGGNPVSH-----QDLGKDAHWFDGDGMLSGVAF---RKASIDGKTIPEFVNQY\n+ILTDLYLSR-KTTSIASPIMPSITTLVNPLSTMFQIMFATFRTIFLVILSNLPGSQ----\n+QAIKRISVANTAVLYHDGRALATCESGPPMRIQLPSLDTVGWFDG-VEAEGE-PEIS---\n+--QAGSDDSPF-GGSGIFSFMKEWTTGHPKVDPVTGEMLLYHNT-FMPPYVHCSVLPKSN\n+EKAP--------GHRLVNQPVLGVSGARMMHDFGASRSHTIIMDLPLSLDPLNTMK--GK\n+EVVAYDPTKPSRFGVFPRHLPSSVRWFHT-APCCIFHTANTWDS---------------Q\n+SSEGELSVNLLACRMTSSTLVYTAGNIRPPVRSR--------------CTQARVWSDERE\n+ETACRYKEAPALESPG----ESTGLADYFPITAESDDYDQCRLYYYEF------DL---A\n+MESRNHVKSQWALSAIPFEFPSVRPDREMQEARYIYGCSTS--TSCFGVALGRADKVDLL\n+VKMDAKTLIQRGKK----MNATSITG----CVDRRSVCEILQ--------------EQRK\n+DDPIYIFRLPPNHYAQEPRFVPRACSTE---------EDDGYLLFYVFDESQ-L-LPSGD\n+CPPSATSELWILDAKNMRD-------VVAKVRLPQRVPYGLHGTWFSSQDIESQRSVESL\n+RSLEVVQRK----------------------KEEWVNSGGQIRKSWMVLREKLEKAVG--\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------\n+>Fgr\n+------------------------------------------------MDSFQKTVPETV\n+SLSHPKEQSPPQPPRH------------PYLIGNFAPIH-KTLNLTPCTH-SGCIPPELT\n+GGQYVRNGGNPVSH-----EDLGRDAHWFDGDGMLSGVLF---RKGTFDGQIVPEFVNQY\n+ILTDLYLSR-KTTSVMSPIMPSITTLVNPLSSLLKIMLATFRTMFLVFLSNLPGSQ----\n+QALKRTSVANTAILYHDGRALATCESGPPMRIQLPSLDTVGWYNG-VQAEGE-PEQT---\n+--ISEDKIEPF-GGDGVFKSMREWTTGHPKVDPISGEMILYHNT-FIQPYVHYSVLPKT-\n+--NV----QAPTTGRLVNQAVPGVSGARMMHDFGASRAHTIIMDLPLTLDPLNLAK--NK\n+EVVSYDPSKPSRFGVFPRHEPSKVRWFQT-APCCIFHTANSWDTKF--------------\n+ANGT-SSVNLLACRMTSSTVVYTAGNIKPPAKPK-----RSNPRSYLAAQDVGQWDE---\n+KDVRRFEAAPMLESPS----EKAHGDDYFSPSDDVDDYSQCRLYYYEF------NM---S\n+ATSTNNVINQWALSTIPFEFPSVRPDREMQDARYIYGCSTS--TSCFGIALGRADKVDLL\n+VKMDAKILIERGKK----MNTRPVTG----CVDRRSAREILD--------------SQDE\n+KDPIKIFRLPPRHFAQEPRFVPRAGATE---------EDSGYLLFYVFDESQ-I-LPNGD\n+CPSSSASELWILDAQNMRD-------VVAKVRLPQRVPYGLHGTWFSAKDIQEQRAVETL\n+RSLEAVQRK----------------------KDEWANNGGSIARAWMTFREKLERAVG--\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.007.AA.only_seqs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.007.AA.only_seqs Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,286 @@\n+>Rgr\n+MGARPHPFREGNYAPVRDERQLEPCTCEGELPLELAGGMYVRNGGEPALAESMRDDAAPA\n+YHWFDGDGMLTGVYFQEARTATGRRHLVPTFVNRYVLTDVYLASHALGLKTPILPSIATL\n+VGSIWTLPLILLAIFRAVFLAFLSFFTHSPLRHLSVANTSILWHDGRALASCESGPLTWV\n+TLPALDTVGYWSLEGDDGEPGLREGMIGWMKEWTTAHPKRDPTTGELMLFHMTFLPPYLH\n+YSVIPSTPAASEKAEPTPRILAAPVPISSPKMMHDMAASREHSILLDLPLSLNPLNLAVG\n+KPMIHYDPAQRSRFGVLPRHAPDLVRWFEAPPCIIFHTAFAADVYDPHDSTRVDAVELVC\n+CRLNSPRLVYAAGNLDLPVAQALPAGAKEACELYYYSFSMSSPTATSPSHAFPLSSIPFE\n+FPTVPQARVVGPAKYVYGCSIKHGNFDAALGGAAKIDCLVKVNVDALVRRGHKRAEAGKG\n+DSERPVDERTVSEVLAQQTSRTSNDDDVPIRILQMPPRHYAQESSFVPRANPRSEDDGYL\n+LTYVFDEHQLDEATGQPRDGATSELWVVDAWDLETVVAKVKLPQRVPYGLHGNWFTADEI\n+REQRDVASVRSRP\n+\n+>Ssp\n+MPTHPYRTGNYVPLREERSAARCTVISGRVPPELAGGLYVRNGGAPSLTKEDKSDDLQPA\n+YHWFDGDGMLTGVHFATCPADPSTISPTFVNKYVLTDVFLASHALGLSKPILPSIATLLG\n+SFATIHLILFSIFRAVFLAFCSFFTETPLRHLSVANTSVLWHDGRALASCESGPLVEVTL\n+PELDTVGYWSLEGDEGEPGMREGLLGWMKEWTTAHPKRDPFTGELMLFHMTFIPPFLHYS\n+VVPSTSPAASSLHEKRHPTPRILGAPVPIAAPRMMHDCAASRTHTILLDLPLSLDPRNLL\n+SGKPVISYNPSEQSRYAVFPRHSPDQVTWFEAPPCIIFHTAFAYDEYYPSSPSFLDPASQ\n+PRPQDVAAVSLVCCRLNSPRLVYSAGNLTLPPSEALALGAKEACELYYYRFPFPASPLAT\n+PRPSHAFPLASIPFEFPTVPTSRVVGPSRYAYGCSVKHGNFDAALGGAAKIDCLVKANVD\n+RLVKRGIERSQRFAKEGVEEDEELPVDPRSIRQVLDEQTPRAEHGSGGVGAEKGDVEIRI\n+FEMPPNHYAQEASFVPRKTQRGEDDGYLVFYVFDESQLDPETKKPRDDAKSELWVLDAWN\n+MLDVVAKVLLPQRVPYGLHGNWFTRDEIASQRQPPTIRQRPSSMPSPVA\n+\n+>Gfu\n+MKFLQQNSFTQTSMSQPHEDVSPAIRHPYLTGNFAPIHKTTNLTPCTYSGCIPPELTGGQ\n+YVRNGGNPVSHQDLGKDAHWFDGDGMLSGVAFRKASIDGKTIPEFVNQYILTDLYLSRKT\n+TSIASPIMPSITTLVNPLSTMFQIMFATFRTIFLVILSNLPGSQQAIKRISVANTAVLYH\n+DGRALATCESGPPMRIQLPSLDTVGWFDGVEAEGEPEISQAGSDDSPFGGSGIFSFMKEW\n+TTGHPKVDPVTGEMLLYHNTFMPPYVHCSVLPKSNEKAPGHRLVNQPVLGVSGARMMHDF\n+GASRSHTIIMDLPLSLDPLNTMKGKEVVAYDPTKPSRFGVFPRHLPSSVRWFHTAPCCIF\n+HTANTWDSQSSEGELSVNLLACRMTSSTLVYTAGNIRPPVRSRCTQARVWSDEREETACR\n+YKEAPALESPGESTGLADYFPITAESDDYDQCRLYYYEFDLAMESRNHVKSQWALSAIPF\n+EFPSVRPDREMQEARYIYGCSTSTSCFGVALGRADKVDLLVKMDAKTLIQRGKKMNATSI\n+TGCVDRRSVCEILQEQRKDDPIYIFRLPPNHYAQEPRFVPRACSTEEDDGYLLFYVFDES\n+QLLPSGDCPPSATSELWILDAKNMRDVVAKVRLPQRVPYGLHGTWFSSQDIESQRSVESL\n+RSLEVVQRKKEEWVNSGGQIRKSWMVLREKLEKAVG\n+\n+>Fgr\n+MDSFQKTVPETVSLSHPKEQSPPQPPRHPYLIGNFAPIHKTLNLTPCTHSGCIPPELTGG\n+QYVRNGGNPVSHEDLGRDAHWFDGDGMLSGVLFRKGTFDGQIVPEFVNQYILTDLYLSRK\n+TTSVMSPIMPSITTLVNPLSSLLKIMLATFRTMFLVFLSNLPGSQQALKRTSVANTAILY\n+HDGRALATCESGPPMRIQLPSLDTVGWYNGVQAEGEPEQTISEDKIEPFGGDGVFKSMRE\n+WTTGHPKVDPISGEMILYHNTFIQPYVHYSVLPKTNVQAPTTGRLVNQAVPGVSGARMMH\n+DFGASRAHTIIMDLPLTLDPLNLAKNKEVVSYDPSKPSRFGVFPRHEPSKVRWFQTAPCC\n+IFHTANSWDTKFANGTSSVNLLACRMTSSTVVYTAGNIKPPAKPKRSNPRSYLAAQDVGQ\n+WDEKDVRRFEAAPMLESPSEKAHGDDYFSPSDDVDDYSQCRLYYYEFNMSATSTNNVINQ\n+WALSTIPFEFPSVRPDREMQDARYIYGCSTSTSCFGIALGRADKVDLLVKMDAKILIERG\n+KKMNTRPVTGCVDRRSAREILDSQDEKDPIKIFRLPPRHFAQEPRFVPRAGATEEDSGYL\n+LFYVFDESQILPNGDCPSSSASELWILDAQNMRDVVAKVRLPQRVPYGLHGTWFSAKDIQ\n+EQRAVETLRSLEAVQRKKDEWANNGGSIARAWMTFREKLERAVG\n+\n+>Nha\n+TPCVYTGNIPPELQGGQYVRNGGNPVGHEDLGRDAHWFDGDGMLSGVAFGRISPNDGRII\n+PKFVNQFILTDLYLSKKTTAVSSPIMPSITTLVNPLSTLFQIILSVLRTVFLVFLSHLPA\n+SQQAIKRISVANTSILYHDGRALATCESGPPMRIQLPSLDTVGWFDGVQAEGEPEGVESQ\n+LDARRFGGNGALSFLKEWTTGHPKVDDRTGEMLLYHNTFVPPFVHYSVIPSSLSNNSNTP\n+KLKLINEPVAGVSGARMMHDFGASHTQTIIMDLPLSLDPLNLLRNREVVSYDSSKPSRFG\n+VFPRHKPDDVRWFTSPACCIFHTANAWDTIVERKVASVNLLACRMTSATLIYSAGNIAPP\n+NVLSNTENIELEETRSIKENLHGPLGTMCHYEKGPVLESSTSTPNAPNCPSAHASEDNDQ\n+CRLYYYEFDLSTTGKNQVSHEWALSAIPFEFPSVRPDCEMQQARYIYGCTTSSSCFGVAL\n+GKAVKINVIAKIDSKRLIQKGKDMHITPVKGCVDERTVREIIDEDNKDDPIQCFRLPTNH\n+FAQEPRFIPRSSSDEEDGGYLLFYVFDESQLNLSGECPTSAVSELWILDAKSMRNVIARI\n+TLPQRVPYGLHGTWFSHSDIEKQRDVKTFRSLEQLQTKKQKWESDRKQWWCSWVQWGDML\n+EKAVG\n+\n+>Ssc\n+MLWNASLMGHVGRYFQSKEILVYFRTAVDLSYSTFLTFARLFMTFANEKKGGFRKQHPYL\n+HGNFAPIHRTQPLTACTYTGIIPKELAGGEYVRNGGNPVTNGDLGRDAHWFDGDGMLSGV\n+AFRRGKNGGIHPHFVNQYILTDAYLSSISTPSLRAPILPSIATLVNPASTLLTIILRIFR\n+TIFLIILSNLPGSAKAIRKISVANTSILYHDGRALATCESGPPMRISLPGLETVGWYNGV\n+QAEGEPVTELEPSEVFGGSGLIGFMKEWTTAHPRIDPVTNELILFHSTFVAPFVHYSIIP\n+STQHNFLPSKSPRLVNAAVPGVKSAKMMHDFGVSLSHTIIMDLPLSLDPLNLARNEPVVS\n+YDPAGRSRFGVFPRWKPEDTQWFETNACCIFHTANTWDETVYNTFTREDETISVNMLACR\n+LTSASLVFSAGDVAAPIPKANPITNPVEEEQCRLYYYRFSFTQAGNFISHQFALSSI'..b'LRFALPSLQTIGWFDGRRAEGEPEKSEREGFGGNEMMTFVKQCTTAHPRTHSVTGELIAF\n+HASLVRPFVHYFIITKAKSGRQPLLTAPVPGMTSPKMMHDFGVSRGYTVIIDMPLCFNPL\n+NLLKGSPVLSFESSRKSKFGVFPLYQPEAVQWYENNPCSPEGKPVPPKYAEEQQCRLCYY\n+SFPFSPVSHAQPPGTKNQWALSAIELEFPNVSPLSVMSEAQYVYGCSARSVCYSVELGKA\n+ARIENLAKINAIDLIQRGLETQPQPIKGCVDKRSIQEILKSSDPDPIQLFAMLKGWYAQE\n+PRFVPRSNPISEDDGFVLSFVFDESQLDERGSCRDDAIGELWVTDAKDMRTLLARIKLPQ\n+RVPYGFHGCWFSKDEVMARRPYTTRKLTEEGAGSWVCVAMSKLDRIRNCTSPTNWSRREY\n+SVKIASIINNLSFVMTPFSRTNTGLNNELVAVSRSHESNPRARIQTMRDTGNDPAPGTQS\n+HIASSDMLAENTHPWLLALTAVIPTVYASRRGSTSECSPVSFDIVATAENAILSPSYDPS\n+NETSIINFINAMARGEVNPVVGSQNISGSFVINGIYCKPTKKVKKKRNALQILVHGITYN\n+SSMWGGYHFGDRYNWHAYANGEGYHTLAIDRLGHGLNSKALDPHNVIQPMLQVEIYKELI\n+QSIRFNTAANSLRKRFSNIIWVDKKVGHSYGSQIALPLARLCPNLTSALILTGWSSTTNL\n+SEVQKFNLASASTLYPSRFPGLDKGYLAMADEALRAKMFYYGAYDPAIPAFDFANQDIVT\n+IGEFAANAGPFGIPPAAYNKPVMVITGVEDGVFCAQPGVAARECEELLEKTRTDMFPGVP\n+GRKYEYFAPRNTGHDLTLHYSARETFRRAHGFLDKYF\n+\n+>Vaa\n+MFPLHHFQVEELVIHLAGGQYVRNGGNPLANNDPERTAHWFDGDGMLSGVLFRSSTDGSI\n+VPEFVNQYLETDVFRYTKRNKHLTRPVLPSITSLVNPASSFLHIMFEIMRAVLLVVLSQF\n+QSAGATIKKISVANTSVIFHDGRALATCESGPPLRFTLPSLETVGWFDGAKAENEIPTAS\n+SEGTFGGHGPLSWMREWTTAHPRVDPLTNELISYHSTFVAPYVRYSVIQPRHTKSLEASR\n+AKPLSPVRPGPPEYAEEEQCRLYYFSFPLGNDNNDAAIKHQWALSAIAFEFPTVAPAAAM\n+RGRGYVYGCTTGRDTYRGALGKAAKIDHLAKMDVATLIARGEADPPREVTGCVDARTVRE\n+IMAHDDPRDPIRLFGMPEGWFAQEPRFVPRDGAKSEDDGFLLTYVFDEAQLDKTGACRPD\n+AVSELWLIDAKGMRDVVARVKLPQRVPYGMHGNWFSEEDISGQIPDEKLTLGSEEVITLP\n+RDKVV\n+\n+>Ggr\n+MDMSPRMEEVAGETVETRHPYLSGNFAPIQSCLPLTPCSYEGTIPLDLAGGQYVRNGGNP\n+VTNDDQTRAAHWFDGDGMLSGVLFRRVGEKDATIQPEFVNQYLLTDVYCHAKSNKYLRRP\n+VVPSIATLVNPTTSMLRIVFEVFRTVFFVMISRLPGFGRPIKKISVANTNVIFHNGRALA\n+TCESGPPLRFSLPSLETIGWFNGRTAENESIHGNESGFGGTGVKSFMREWTTAHPRVDPV\n+TKELITFHATFVKPFVRCSVVPPTSKPFSGCQPMFDAPVPGIESPKMMHDFGVSRRHTVI\n+MDLPLSLDTMNLLRGIPSLSYDSAGKSRFGVFPRYRPDAVEWFETNPCTIFHTANCWDTI\n+LPEIDNNSPGMSVNLVACRLTSAAMVFSAGNLPTPEVKPVPPEYAEEEQCRLYYYNFPLS\n+NKAGVQYNIRHQWALSAISLEFPSVAPAYSMQEARYVYGCSTGEASYSVALGKAAKIDHL\n+AKLDVQTLIARGLAKPPQPVKGCVDMRNVHQILTSKDPKDPIKLFRMPDGWYAQEPRFVP\n+RKQPRSEDDGWLLVYAFNEAQLDETGECLPDAVSELWIIDAKGMKEVVARVKLPQRVPYG\n+LHGTWFSEDEINEQMPFIQTRGMAQQ\n+\n+>Uma\n+MVKGSSNRRQHSASLQGLPSSQHCAPVISIPSPPPPAEDHAYPPSSFTIPLSKDEELAEA\n+GPSRPGSSAISRRPVLSRRRTSKKEYVHPYLSGNFAPVTTECPLTDCLFEGTIPEEFAGS\n+QYVRNGGNPLANSERDRDAHWFDADGMLAGVLFRRTPKGTIQPCFLNRFILTDLLLSTPE\n+HSRLPYVPSIATLVNPHTSVFWLLCEIIRTFVLAMLTWLPGLGLGGNQKLKRISVANTSV\n+FWHDGKAMAGCESGPPMRIMLPGLETAGWYTGEEDKEKETCDKNSGNSLTSSSSKGFGGG\n+PPIVSMLREFTTAHPKIDPRTQELLLYHMCFEPPYLRISVIPASQSKKTDLPAHAKTIKG\n+KAVRGLKQPKMMHDFGATATQTVIIDVPLSLDMMNLVRGKPILHYDPSQPTRFGILPRYE\n+PERVRWYESAEACCIYHTANSWDDDGKFDASHEHATRSAIRGVNMLGCRLNSATLVYSAG\n+NLLPPSHVLPPPNCPEKCQLYYWRFDLEHAETNTISHEFALSDIPFEFPTINEDYSMQQA\n+CYVYGTSMRDGTFDAGLGKAAKIDALVKLDAQALIRKGKAMWSQGRLKAGDSVDTRTVEE\n+VLTAQRDGSASPEDPIKIFEMPRGWYAQETTFVPRRSSTNETSQEDDGWLVCYVFDEATG\n+LHPSTGEVLPGASSELWIIDAKLMSRVVCRIKLPQRVPYGLHGTLFTEEQIASQKPIDPS\n+QVRSWALSINLADPFSSSALGSTVYSAAGKAATSKFKNREETYAAFIKDPIRIGAWWVKR\n+NIELLIA\n+\n+>Sma\n+MDMPLSLDPVNMIRGKIVLSYDGTGKARFGIFPRYHPERVQWFETNPCCIFHAANCWDAI\n+SEEDSNIPEDVEPTTTVNLLVCRMTSASLIFNTGNLPTPVSKTPIPSKYHEEEQCRLYYY\n+SFSLVPRSQRIVHQFALSAIPFEFPTLSPAHTMTQARYIYGCTATSPSASYTNSLGKSVK\n+IDALAKIDVSVLIARGTATNNPSPPEPIKGCVDTRSVSEILTSPSYSSSEEDDPIKIFTF\n+PPNHYAQEARFVSRHNGISEDDGWLLTYVFDESQLNEESAECMEGAKSELWIIDAKGMRE\n+VVARIRLPQRVPYGFHGAWFGEEEVLGQRGVEKVRKIEDMDGGEGGFWRVVKQCIGRWLL\n+R\n+\n+>Mlp\n+MITPFINQLHSKLSLLSDHPNVKHSSQDKIKPSSIHPFLSGNFAPVHIEHSLTLCQFSGG\n+LPDELVGGQYLRNGANPLHLPTPDQPYHWFDGDGMIHGVYFSSSSAPLYVNRFVDTDIYR\n+ASKRRGNSILPSIASLISPISSPASLLATILRAVFINWLSNVSRLTVANTALVFHDRRLL\n+ATCESGPTVAIHAPQLDTIDYHVFPDEATGKNGLGQAPLVVGAESTAAGHPIGGMLEEWT\n+SGHPKVDPINGELVFIGCNIFARPFVTHSVVSHTGHHVSFKKPIHDVIQPKMMHDFGASH\n+GHTVILDLPLTMDPINLLKPGAPPIVHFDRTLSSRFGVLPRYDPTATRWFTASPCLILHT\n+ANTWDSTRSSTLRDLGLRSKESEHENYVAVNMLACRFRTAKLVYTAGDLEPPLAEQTDQD\n+IVRLTYYRFSLSEDDPLWSGPDSITQPSHLFALSAIPFEFPVLPPNKLMSEVQWVYGCSM\n+ASGSFDAGLRGGARPNVLVKMNVRELIKRGIKSVKSGKTGPKDQDGIFEVDSRTMPDLLK\n+SEPDSSIRLLELPKGFYLQEPSFIPRKEATREDQGWLVCYVFDENQLEENGQASLKAYSE\n+LWVLDAELIGEGRSWEEVLVCRVRLPSRVPYGLHSTFLNSEEIQNQRSNSRSNVRLHEHE\n+KNGKVVLASRFQEGLVWVFGGEDELEDL\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.009.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.009.AA.fasta Fri Mar 25 17:10:43 2022 +0000

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.010.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.010.AA.fasta Fri Mar 25 17:10:43 2022 +0000

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.011.AA.YKL197C.clw
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.011.AA.YKL197C.clw Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,852 @@\n+CLUSTAL W (1.83) multiple sequence alignment\n+\n+\n+Spo-PEX6_SCHPO -QLMESFINQNVCQPFVIERKDSFTFLASNEKNISSFKTETDAELVIRPS\n+Spo-O74941 -YAEIELEIEPDWEILLVQVATTFIQFQPLKLIPSSLCLLRTTEVLITPK\n+Cel-O16270 -TCSNIRVMKVSVKINLFGLVKNVAVDNITPNFKFHETISEDAKLSLMRQ\n+Cal-CA3485 -IVDIPLSQIFEYQLKFLTLVDNGNVVNEGDSIRLILTVEYDTNIVLINQ\n+Sce-PEX6_YEAST -LYMETVHSRDLCQIDFTELILEYALPKIGTNSALSDLPCTISRDLLRPA\n+Dme-AAF58736 LIESPVNFVNGRRVN-MTQIKQENFYGNILDRFQIRNCVEHFADEQTIPG\n+Aga-SANGP00000018134 -VANLVKVAKCEPTPKQDVLCQENLVENLNERYTRHRYLQRITEGQHLPA\n+Ath-Q9SA70 -----LLSTKDLFWIFLKCVVKIEIGIQRVAQVVVLDPTLEDASLTQVPV\n+Ncr-NCU08373.1 -LADATTLCEPDLDETVTGTIGPGSVISSYTATTARKAMKPIPPDLLHPK\n+Hsa-IPI00103761.1 -LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPP\n+Hsa-IPI00299182.1 -LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPP\n+Rno-IPI00188277.1 -LLRRPALGWASPGPRRGEPVPGLLGPGTRLAVTELQGLDPESRDHNHPP\n+Mmu-IPI00116764.1 -LLRRPALGWAAPGPRRGEPVPGLLGPGTRLAVTELRGLGQESRDHSHPP\n+Ncr-NCU08118.1 -LAMATVNIEPDWEMLLFQAIPSKANIKVISIDPPLPCIAPDAEIIVAPK\n+Mbo-CAD93306 -AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGS\n+MtU-P96281 -AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGS\n+Mtu-P96281 -AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGS\n+Aga-SANGP00000014403 -----VVGTVRTLWPG-AKVEFNDVSANELNATVTTLDLEDAEEIFLRLE\n+Dme-Q9VK63 -----AMQPLRIVWPEQFKLHCTQLRGKLLKISALHPSLTAAASISLKHV\n+Sto-Q96ZY0 --------------------------------------------MNANTS\n+Sso-Q97V06 --------------------------------------------MATVTS\n+Aga-SANGP00000019182 ----------------------GICGVTQGPSVYG--EVDRHTVIKIDQI\n+Sso-Q97W25 --------------------------------------------------\n+Hsa-IPI00031608.1 -ALGSCCTAWPADGFAAVGASRSRRSLSL-NRLLLVPCLRRVAVWPVLRE\n+Fru-SINFRUP00000053015 -LMGSCCTAWPAEGFSLMSHPPTQLQMDH-SKITPVTCLRCVKTT-VIVG\n+Ath-C48B_ARATH --------------------------------------------------\n+Cal-CA5106 -ILSDSSAGVVSNDITISFPYRQLCGLLLGDRVELVKFPQYASDISISGV\n+Sce-AFG2_YEAST -VLIGEGILVIDEEVTLSTTIRSVGNLILGDRLELKKAPPYATKVTVGSL\n+Spo-O60058 -ALGEAGITQSGIGPLISPLLAKWANLKAFQRVNISQYLKEAEGIKIVAS\n+Ana-Q8YUT8 -----------------------DLFKGFEQLIELVKTLEEKAEIKTD--\n+Ecu-Q8SSJ5 -TLKKALIFSTSVPPAIVRDGRFNLRIRITDTVKLYRVIPVVSKLNFLPI\n+Pfa-MAL6P1.232 -RMKRHTICIIDLDERINKVARKNLRVCLGDVVYVKSCIPYGKKIQVLPI\n+Gth-Q98S05 -KIKKKTVCIINCELRINKTVRENLNIGIGDIVTIHHFLKFGKRIHVLPF\n+Ath-C48D_ARATH -TMKRKTVCIATCDERMNKVVRSNLRVRLGDVISVHQCVKYGNRVHILPL\n+Ath-C48A_ARATH -TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPV\n+Ath-C48E_ARATH -TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPV\n+Cel-TER2_CAEEL -KMKRRTVSIVNCPNKMNKVVRNNLRSRLGDVVSISSALEYGKRVHVLPI\n+Cel-TER1_CAEEL -KMKRKSVAIISCPNRMNRVVRNNLRIRLGDVVSITPALSYGTRIHVLPI\n+Fru-SINFRUP00000067653 -KMKRRTVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Rno-IPI00212014.1 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Mmu-IPI00122342.3 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Mmu-IPI00318619.1 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Hsa-IPI00022774.1 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Dme-Q9V3C3 -KMRRKTVCIVTCPDRMNRVVRNNLCVHLSDVVSVQSCVKYGKRVRILPI\n+Aga-SANGP00000022801 -KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPI\n+Aga-SANGP00000021747 -KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPI\n+Ncr-NCU00018.1 -TMKRKTVLIVDLDDRLNRVVRHNLRVKHGDIITIHPCIKYAKRIAVLPI\n+Spo-CC48_SCHPO -TMRRKTVLIVEMEDRINRVVRNNLRVRLGDIVTINPCIKYAERISVLPL\n+Cal-CA3333 -TMKRKTVLIVDMPDRVNRCVRNNLRVRLGDIVTVHPCIKYANRISVLPI\n+Sce-CC48_Y'..b'FNDFIKILANVKPSVNKETLKMYEEFIQRI\n+Sso-Q97V06 VKLEDFMDVLKRVKASLDRQTLIMYEKFFERR\n+Aga-SANGP00000019182 VTMAHLRSALQDVRPSLTKEQIDWYHSYANRL\n+Sso-Q97W25 LTREDLIDALNKIHPSVKKRLSKGSSSNDHET\n+Hsa-IPI00031608.1 VKQEHFLKSLKTVKPSLSCKDLALYENLFKKE\n+Fru-SINFRUP00000053015 LKHRYFVQALSRMRPSLTEQQINSYQ------\n+Ath-C48B_ARATH VFNRHFQTAKSSLKPALTIEEVETYSSFRKAA\n+Cal-CA5106 VTNKHFEHALKGISRGITPEMLEYYEKFSKKS\n+Sce-AFG2_YEAST VELRHFEKAFKGIARGITPEMLSYYEEFALRS\n+Spo-O60058 ICQAHFKTALLALRKAITRDMLEYYASFSESV\n+Ana-Q8YUT8 ITTDDFNYAYKVLTEQRPD-------------\n+Ecu-Q8SSJ5 LRPDHLVQSLKTARRSVSEKEVERYEAFARSM\n+Pfa-MAL6P1.232 ITRHHFKEGLAGARRSVSQADLIKYDNFRIKF\n+Gth-Q98S05 ITKEHFLEAMKYARRSVSDSDIRKYEMFAQKL\n+Ath-C48D_ARATH IKAGHFEESMKYARRSVSDADIRKYQAFAQTL\n+Ath-C48A_ARATH IKAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+Ath-C48E_ARATH IRAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+Cel-TER2_CAEEL ITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+Cel-TER1_CAEEL ITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+Fru-SINFRUP00000067653 IRKDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Rno-IPI00212014.1 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Mmu-IPI00122342.3 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Mmu-IPI00318619.1 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Hsa-IPI00022774.1 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Dme-Q9V3C3 ITSAHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+Aga-SANGP00000022801 ITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+Aga-SANGP00000021747 ITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+Ncr-NCU00018.1 LTKRHFEEAMSMARRSVSDVEIRRYEAFSQQM\n+Spo-CC48_SCHPO VQRHHVEEAMKMARRSVSDAEVRRYEAYAHQL\n+Cal-CA3333 ITRAHFEEAMKTAKRSVSDAELRRYESYAQQL\n+Sce-CC48_YEAST ITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM\n+Hal-Q9HPU1 VTMAHFEAALGEVTASVDADVKENYEEIEQRF\n+Hal-Q9HHW2 LSIEHFEQALEEVDSNAGSETQAFEKPAEAV-\n+Hal-CDCH_HALN1 VGMAHFRAAMENVRPTITDDLMEYYDQVEDQF\n+Mma-Q8Q089 VRQKHFLQAIEETGPSVTPDTMKYYQAIRGEL\n+Mac-Q8TPU1 VRQKHFLQAIEETGPSVTPDTMKYYEAIKGEL\n+Tac-VAT_THEAC VSQKNFLDALKTIRPSVDEEVIKFYRTLSETM\n+Tvo-Q97A35 VSQKNFIDALKTIRPSIDEEVIKFYKSISETM\n+PaE-Q8ZTN5 VSMKHFEEALKRIPPSLTPEDIRRYEEIAKRL\n+Ape-Q9YC86 VEMRHFLEALKKVPPSLTKEDILRYERLAKEL\n+Sso-Q97ZZ9 ITMQDFLDTMKIVTPSLTKADIMRYENMVKEI\n+Sto-Q975P4 VTKEDFNKALEVVKPSLTAADIQRYERLAKEL\n+PaE-Q8ZYN4 VSMRHFEEAMKKVRPSITPDMLKFYESWLEKA\n+Ape-Q9Y910 VSMRHFEVALKKVKPSVTPQMVEYYKRWLETV\n+Sso-Q980U9 VSLRHFEEAMRKVKPSVTQDMLQFYQNWVEKA\n+Sto-Q976H7 VEKRHFDIALKKVRPSVTMDMIQFYQNWLEKA\n+Pab-Q9V1N2 VTMKDFEEALRKIGPSVSKETMEYYRKIQEQF\n+Pho-O59515 VTMKDFEEALKKIGPSVSKETMEYYRKIQEQF\n+Mth-O27676 VSMKYFLEAMEKVKPKGGVEEQVQYH------\n+Mja-YB56_METJA IKKEHFMKALEKIKPSVSKEDMRVYEKLAQEY\n+Afu-O28972 ITKKHFEEALKKVRPSLTKEDVEKYEKLIEDF\n+Mma-Q8PXG2 LSKRHFEKAIRRVKPTTSRETLSAYEKSAELF\n+Mac-Q8THE2 LSKRHFERAIRRVRPTTSRETLSAYEKSAELF\n+Sce-YL34_YEAST VTMSDFRSALRKIKPSVSDKDRLKYDRLNKKM\n+Spo-O14325 VTNADFELAFKNIKPSVSDRDRQKYQRLAKRW\n+Ath-C48C_ARATH IKTRHFEQALSLVSPSVNKQQRRHYDALSTKL\n+Ath-Q9FXH9 TKMVHFEEASSRMQSGR---------------\n+Sce-PEX1_YEAST VTINDLLEACQETKPSISTSELVKLRGIYDRF\n+Cal-CA3667 ITHENFLESLKETKPSISHSEKIKLTKIYKEF\n+Hsa-IPI00296368.2 ISQSHLMTALGHTRPSISEDDWKNFAELYESF\n+Fru-SINFRUP00000064701 LSAAHLNAALAVTRPSLSRDDWNRYTNLYEAF\n+Ath-Q9FNP1 ITDPLLKSIASKTKPSVSETEKQKLYDIYSQF\n+Dme-Q9VUC7 LKQKHLIESFQTTRPSLSASDVAKYHRTYARF\n+Aga-SANGP00000012419 VSQRHLAEAFSSTRPSLSPRDIAKYRETYARF\n+ . \n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.011.AA.YKL197C.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.011.AA.YKL197C.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,747 @@\n+>Spo-PEX6_SCHPO\n+QLMESFINQNVCQPFVIERKDSFTFLASNEKNISSFKTETDAELVIRPSFDENESVISEE\n+GTFLVARGPSVGIASRFCVPANSDVDRNTDAYIWYSVEEIDPIVQLSHRLLPSLRKPLLN\n+FVKVHPPSQKLLRFCRADPQQVFLLHGNPFTGKTKAVEEVASLFSFVKDLDVLSI---SS\n+GNIVPKSIQILLSKIDLVKPQGYIVIGTCHSIEKIPYEILSESFFELKFSELEMDERLEL\n+LKIYANNVIIDKRISLKDVALKTNSMSFGELECLPDHMTKAAVDRIKSGPIITEQDVDVS\n+INRIRKE--KSNTFTVPKVNWDDIGGLEEAKTVLRDTLQLPLNVRNVFEKARNSSPCVIF\n+FDELDSIAPHRGSDSGNVMDRVVSQLLAELDSISKKASMLRALTKTFKLDETIDLNEIAK\n+CHPNFTGADMYALDSLELRITKEDFLTSLKKLRPSISEQELHRYEMVRHQF\n+>Spo-O74941\n+YAEIELEIEPDWEILLVQVATTFIQFQPLKLIPSSLCLLRTTEVLITPKDSVADSLCVFL\n+PLNFPDRPDVVYMDGGFKFQPSSSFILPPESNLSLVAAKLKNAVVSGLS--GVVKNPIQD\n+IIRNNSPRLPFPHEFAQNAVFHIYINGPKGCGKSNLVHSLFDYYSYLDDVHCLISSSGEL\n+GFVEEREIAFLQHQIINLKRKRIIFIGFGEEFLTFSENLVLPFQIKIALPSLAVTRRKEI\n+LTIFQENF---SDMDIEFISVKTEGYLMTDLVLFVKRLLSEAFVEKINKGLI-----EKT\n+LKDFVPLQLRKKFVK-SSIRWIDIAGMQEAKEAVRDIIESPVGVRDLFSRAQMAKPCVLF\n+FDEFDSVAPRRGQDSTGVTDRVVNQILTQMDGAESRLEVLQKLANRFHIENAAMLKKLST\n+LTDGYTYADLSSLDSKSVVIEDYMLMEALKKNSPSLNSEEFEHLSNLYRDF\n+>Cel-O16270\n+TCSNIRVMKVSVKINLFGLVKNVAVDNITPNFKFHETISEDAKLSLMRQNIREKHHLKQI\n+LKNVFYKNDVIRITNYLFYKDVSSPCIMDSSTAVYETSAVSQ--SLPFSNFLLKNSLTSS\n+MRTTV---FRMTQIYSATISKKLLVTGASGSGKRLMSRVFASETHFIRNSNVL----DQF\n+NALDRRILQYMEQKLSE-PSKIVIFSCNTDTMSSMPANVKNLALYTFSAEFMDENDRKTW\n+LQYYL------NEKLANHVAKKTSGFTLAELEKLVKNGKKVKIEEKEEKV------YEDL\n+IDKRNSNFADAGAPKIPNVRWEDVGGLEETKQTVLESI----NLRKVFERAKQASPCVIF\n+FDEIDSLAPNRGGDSGGVIDRIVSQLLAELDKLHNKTKILEAVSRKMRFEEDVDLREIAS\n+VDEKMSGAQLFSIENQSIRVAQRHLLESVKRFHET--------------KY\n+>Cal-CA3485\n+IVDIPLSQIFEYQLKFLTLVDNGNVVNEGDSIRLILTVEYDTNIVLINQSELVFINNADF\n+IKFPIFNGDLVVVRVFLDTLKTYQSFTTLSTRLKVIDTVLAKIGAVAWFEVGANSIDTNQ\n+FVESIRLPQSFVKWYQYNLPPFILLTSMSGIGKTTLVRNSCIELGYLKHIENLCPKTDQN\n+SSIFTSLSLKIIVLHDYLKTYRLVIVMSCNDYDKLNDNLKSIIKFTIEFTVPSENERLEI\n+FKLINNEKNKTKDINFKNLALQSAGLTPRDLISIIKKSKKLAIKRLTVNIVIVPDDFNAA\n+INEARNQFSDSGAPRIPNVKWEDIGGLDLVKDEILDTIDMPLNVRRVFQRARDAKPCVIF\n+FDELDSVAPKRGGDSGGVMDRIVSQLLAELDGMSSKTKILEALTRKFKLDDNVNLEQVAA\n+CSFTFTGADFYALQDTTVLVQMEDFIKAQNELIPSVSAEELQHYLKVRENF\n+>Sce-PEX6_YEAST\n+LYMETVHSRDLCQIDFTELILEYALPKIGTNSALSDLPCTISRDLLRPAVKLVLLLPNGF\n+KKRTIYAPPKIIASFPIILTMADLIASDDEDELGYKNDSLVWRTTTNITPLPLSRSNLQR\n+YYDLHIFPYVRQLVNILSFNCQVLLHSTTNVGKATMVRFASKYLGFLAHLDSILLDVNQD\n+PEAIKKSINFEMKLLDDFTFKPTTFVGSVNNIDNVPSSFRSHMRFEILVPVPSEAQRLRI\n+FQYLSQKVPVSDNISFSSLSSYSAGLTPLDIKSIVETARMTATARFYQSILITQEDLSKA\n+TSKARNEFSVSGAPQIPNVTWDDIGGIDFVKGEILDTIDMPLNVRRVFQKAREAKPCVIF\n+FDEIDSVAPKRGGDSGGVMDRIVSQLLAELDGMSTKLNILEALTRKFVLDNDVKLIELAK\n+CPFNYTGADFYALEDTKVVVKMEDFLKAQEQLTPSVSRAELNHYEAVRANF\n+>Dme-AAF58736\n+LIESPVNFVNGRRVNMTQIKQENFYGNILDRFQIRNCVEHFADEQTIPGPAETEVILSNY\n+FNRLMHRGHTYRIEVNVHLKTKGSFEAKNFSN-------LVQVPASHSFYPSGLRKPYKL\n+LRSSVDAFLPKKSACLSHIFPVFLLQGERGSGKSKLVSAVAQELGCFHNFEIF----DNE\n+GNEDLRLLSAFHVQVQELFDRKPIVVVALTSDRHLKPMIQGLFLEIINIDMPSKEERFEI\n+LRMHVEQLPLFPRLNLQDVAAKSQGFLLGDLQLLYDNAVRMKIRNRLGRTTLDMSHFAKN\n+LTDMQSSFADSGAPKVPKVYWSDIGGLAKLKDEIQSSIGLPLNVREVFSRARSAAPCVLF\n+LDELDSLAPNRGGDSGGVMDRVVSQLLAEMDGMSDKAAVLRAQTQRFALDAGVDMEQIAE\n+LKSEMSGADLYSIVPENVIVQEEDFTKSFNKFVPSISAKDLEYFNNLKASY\n+>Aga-SANGP00000018134\n+VANLVKVAKCEPTPKQDVLCQENLVENLNERYTRHRYLQRITEGQHLPASSDVDFILGRY\n+FERLLYRNHTYQVPLTLWFKSTAGFEIAQKSLTTLQQTTTYNLPDGPYMRPFGLRKYFHS\n+LRSSLQAYLKMENNGLVGIYPVFMLRGERGIGKMAVLRSVASALGCLENFEVF----DNE\n+GHEDQRITGSFQAELMTLFGRQVVVVAVANQKESNTPKLTSLFLEVIQLHAPTTAERLEL\n+LRWISYRLPVAQ---LQKIAEQSQGFTLADLELLYGNA-LEAWRRSQDTGRVGLNHFLAL\n+LDHMQSTFSDSGAPKVPKVLWSEIGGLAKLKSEIQNSIGLPLNVREVFARARTASPCVLF\n+LDELDSLAPNRGGDSGGVMDRVVSQMLSEMDGISKKESVLRAVTGRFRLAETLTLRKIAE\n+LKQDMTGADMYSINADQVIVTEDDFKESVKKFIPSISPADMAYFNQLKGNF\n+>Ath-Q9SA70\n+LLSTKDLFW----IFLKCVVKIEIGIQRVAQVVVLDPTLEDASLTQVPVMLVPTYMGQQL\n+LDSLVHRGNGVLEKYFVSFVDSALKYQLSRGDIFSICNPCSQNERVNHSQTSGLPPDLLV\n+YRSKVPMPLETVNILASSPPLPVLLHGIPGCGKRTVVKYVARRLGLLRHFDVFQDGSDRV\n+GVSFESVIRELTPVSNGDSSNGVLLIASAESTEGISPTIRRCFSHEIRMGSLNDEQRSEM\n+LSQSLPKLQISSDEFMKGLVGQTSGFLPRDLQALVADAANLYISQESHQANSAKEDFTKA\n+LDRSKKRNASAGAPKVPNVKWDDVGGLEDVKTSILDTVQLPLNVRDIFEKARSARPCVIF\n+FDELDSLAPARGGDSGGVMDRVVSQMLAEIDGLSDRERVLKALTRKFKLSEDVSLYSVAK\n+CPSTFTGADMYAL'..b'----------------------------------------\n+--------NVFKRSQFLFYFMHLVVA------------------SLHW------------\n+-----------------------------------LVHAIANETGFIDEIEAIASKRHQQ\n+KGMETRIVTQLMNY---------------------------------------EKAREEI\n+LTLILRNRPLDPSFDIARIVRKTSGFVGADLALLVKEAANVAMERLVEKLFYTISDFEEA\n+LKKFKPSLTREGFSTTPSVTWEDIGGLDHIRKEFYSDIIKPLAIRELFNLARMCSPCIIF\n+FDEVDALTTKRGGEGAWVVERPLTQLLNEMSGGKERGLILKSLARKIPLDTSVDLDAIAR\n+RCENFSGADLEALGSYPRRTKMVHFEEASSRMQSGR---------------\n+>Sce-PEX1_YEAST\n+LALATVYVTPDWEIEILHRIVIVTKFKIDRVEPSMKSITDGSLVVVAPKQKGASIVKCSL\n+RQKSDSDNKSVGIPSKEFLQSGDQSKLLTNNIIECNLNEISNLPHV--KETGEVSRTSKD\n+EDDFITVNSIKKEMVNYSPIITIILDGKQGIGKTRLLKELINEVEVLDNVEALANDGSNN\n+GQWDNKLLNFFINQVTKIFNKDIRVLFSGKQKTQINPLL--FVSETWSLRAPDKHARAKL\n+LEFFSQIMKLNRDLQFSDLSLETEGFSPLDLEIFTEKIYDLQLER---DCVVTRELFSKS\n+LSAFTPSALRGKLTKETNIKWGDIGALANAKDVLLETLEWPTNIRELFERAQSVKPCILF\n+FDEFDSIAPKRGHDSTGVTDRVVNQLLTQMDGAEGRLDILQAIVKKFALEKNADLKLIAE\n+KTAGFSGADLQGLSTSAAVVTINDLLEACQETKPSISTSELVKLRGIYDRF\n+>Cal-CA3667\n+FAESTINLEPDWELLLSQCVATSAKLLVTDLGSTDHTISPYCEIAIAPKVAGFVYIDDEL\n+PQNSEYVA-VSVIPGPVDYKNQIGIIIKNLPIIHTKKKEITIIAITNFTKIGGLLRFRKN\n+DKKPIKFEILRPSSFIEEIDKPTLVYGNSGSGKTLLLKLVAQQLNILDNIDKLMSVENMD\n+ATKSNQLTEFFISNLTKIHHQLLSILLSANSKDNINKLL--LIENFHHLNPPDKSLRFEI\n+LDKYLNKLGLKIKVDLMDLVSETEGYLPNDLKILSDRIYHEVLFNSTTNAAVTSEHIEKA\n+LAGYTPSNLRGVKLQKSSINWSDIGGLKEAKNILLETLEWPTSVRELFERAQAAKPCILF\n+FDEFDSIAPKRGHDSTGVTDRVVNQMLTQMDGAEGRLDILQSITTKMDLSDDVNLHEIAE\n+KTTGFSGADMQGLNKSKVLITHENFLESLKETKPSISHSEKIKLTKIYKEF\n+>Hsa-IPI00296368.2\n+VGSCQVEVEPDWEILLDQIVFTYIFIQIVALIPAASYLETDTKLLIQPKCVLVVWLEELN\n+NADDLRKRLNINLPKDKEFSEKDKIFLLQKTTIQVIAYPMVKLPFLKLSSLGGVNSLGVS\n+SLEHITHSLLSRQLMSLGLRNALLLTGGKGSGKSTLAKAICKEFDLLDDLDLIVPEHEHS\n+PDAVQRLAHALNDMIKEFISMGVALIATSQSQQSLHPLLVSAFQCVQHIQPPNQEQRCEI\n+LCVIKNKLDCDTDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSRQSEKLVLTTLDFQKA\n+LRGFLPASLRSNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAAVRDIFIRAQAAKPCILF\n+FDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGRLEILNVLSDSLPLADDVDLQHVAS\n+VTDSFTGADLKALNQPGPAISQSHLMTALGHTRPSISEDDWKNFAELYESF\n+>Fru-SINFRUP00000064701\n+LGSVHVFVEPDWEILLDQVVFTVIYILIASLSPSVPYLEQSTELIVSPKVVVVVCMDSYW\n+NGSPLAIGWNVPLPLQLEFVDPPDLFVIQKN-IQVNNQPLLRLPSLSV--LGGIKDLSET\n+GYEFISNSLLSQVLCQNGLKGALLITGAKGSGKSSLSKALCGERELLDDLDQISPEHEHS\n+PEAVQHVAQSLMDVVDEMVLRSVCLIITSLSERSLHPSLTEAIQGFVRLQLPDQAQRAEM\n+LRLILRKNCISQVLDLAALAKETEGYTPQDLAVLLERAHANVVQRGSDGLCLSQRDFMQA\n+LKGFTPPSLWGDLCTPSGVGLDRVGGLKEVRQQLMDTILLPAAVRDVFQRAQAAKPCILF\n+FDEFDSLAPRRGHDSTGVTDRVVNQLLTQMDGVEGRVEILKALSAGVPMATDVELEKLAA\n+ATEQFTGADLKALLRPGLLLSAAHLNAALAVTRPSLSRDDWNRYTNLYEAF\n+>Ath-Q9FNP1\n+FAKATVTVEPDWEVILSQILHTVIRFSVVSTFPSKGVLVPGTEVAVAPKSPCFKINEKVL\n+DKDRLGNNNSVSSHPPLEYLDAMAVTSLIVGGLEIDGQPSVNEPKMNLGYLKGVSPDISS\n+LMTVLLSPAA-GMWFSKKIPSPILIYGPPGSGKTILARAAAKYEEILDDLDSIISSSEGT\n+QASVGMLTKFLTDVIDDYGSCGLAFVASVQSLEQIPQTLSSSFDFHVQLAAPATSERGAI\n+LKEIQRLLDCSEDI-LLNLAAKCEGYDAYDLEILVDRAVHAAIGRHLESNNLVKEDFTRA\n+MHDFVPVAMRDTKSEGGRLGWEDVGGVTDIKNAIKEMIELPSAVRDIFSKAAAAAPCILF\n+FDEFDSIAPKRGHDNTGVTDRVVNQFLTELDGVEVRLEILTVLSRKLLMADDIDLEPIAL\n+MTEGFSGADLQALTGTTPIITDPLLKSIASKTKPSVSETEKQKLYDIYSQF\n+>Dme-Q9VUC7\n+AANLRVHVTPDWEIVLEQIVNMQVALTVDRLKPHMNYIDHNTELVVAPNVRVTVEIEDDL\n+PEHPSIELNANLMKLLFKRFQHKPLFVRLEDPEHLKESKIYATPPLSVQDLPEYDKIVDQ\n+VVQELRMNL----CLSASVMRQVLLAGASGTGKTVLVERILDQLSVLENLDVLAHAAQSS\n+QDGEYRMADTVYQLIVQYTTNNIAVIATVNELQTLNKRLSSPFQTVARLPNLERADREII\n+LRELCSHINVAKDLDLVKFSNLTEGYRKCDLVQFVERAIFYAYRISKTQPLLTNDQLIES\n+LEHTNSYCLQGQSNQANEMRVEELPGLESVVGVLEEVLMWPSNVRNLFNRARSARPCVLF\n+FDEFDSLAPKRGHDSTGVTDRVVNQLLTELDGVEGRVRIFEALSSTLSLDECVDFDWFAG\n+KTANYTGADIQSILAKKISLKQKHLIESFQTTRPSLSASDVAKYHRTYARF\n+>Aga-SANGP00000012419\n+LVKI--------------------------------------------------------\n+-------------------------------------------------------EKIER\n+IVEECTDRLKYALCLDAKVPQQMFIAGSSQSGRKTVCDNILKRLAFMDGLDVLAHQPQNT\n+PDAEYKVSDMIRKQIEEFTGNNIAVIASISSSSNLNRRLHSSFQQHVKLPNLDKADREAA\n+LKLFVRQCKLDRRIDWKRLANQTEGYAIGSLVQLVDRAVFYAYKQDGEALDVTNRYCLVG\n+IENHKQQATDELEEEDDEVPGDKVPGLEGAIEVFQEVLMWPTNVRNLFDRARSAKPCVLF\n+FDEFDSLAPRRGHDSTGVTDRVVNQLLTELDGVEGRLEIFSNHSKSLTLDKDVDLREFAV\n+KSEYYTGADIRSIVPEQITVSQRHLAEAFSSTRPSLSPRDIAKYRETYARF\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.011.AA.YKL197C.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.011.AA.YKL197C.phy Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,674 @@\n+ 83 471\n+Spo-PEX6_S QLMESFINQNVCQPFVIERKDSFTFLASNEKNISSFKTETDAELVIRPSFDENESVISEE\n+Spo-O74941 YAEIELEIEPDWEILLVQVATTFIQFQPLKLIPSSLCLLRTTEVLITPKDSVADSLCVFL\n+Cel-O16270 TCSNIRVMKVSVKINLFGLVKNVAVDNITPNFKFHETISEDAKLSLMRQNIREKHHLKQI\n+Cal-CA3485 IVDIPLSQIFEYQLKFLTLVDNGNVVNEGDSIRLILTVEYDTNIVLINQSELVFINNADF\n+Sce-PEX6_Y LYMETVHSRDLCQIDFTELILEYALPKIGTNSALSDLPCTISRDLLRPAVKLVLLLPNGF\n+Dme-AAF587 LIESPVNFVNGRRVNMTQIKQENFYGNILDRFQIRNCVEHFADEQTIPGPAETEVILSNY\n+Aga-SANGP0 VANLVKVAKCEPTPKQDVLCQENLVENLNERYTRHRYLQRITEGQHLPASSDVDFILGRY\n+Ath-Q9SA70 LLSTKDLFWI----FLKCVVKIEIGIQRVAQVVVLDPTLEDASLTQVPVMLVPTYMGQQL\n+Ncr-NCU083 LADATTLCEPDLDETVTGTIGPGSVISSYTATTARKAMKPIPPDLLHPKDVQAVMLKHYF\n+Hsa-IPI001 LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPPLGGGDSLGRYL\n+Hsa-IPI002 LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPPDPLMGEIQRYL\n+Rno-IPI001 LLRRPALGWASPGPRRGEPVPGLLGPGTRLAVTELQGLDPESRDHNHPPDPLVGEIQRYL\n+Mmu-IPI001 LLRRPALGWAAPGPRRGEPVPGLLGPGTRLAVTELRGLGQESRDHSHPPDPLVGEIQRYL\n+Ncr-NCU081 LAMATVNIEPDWEMLLFQAIPSKANIKVISIDPPLPCIAPDAEIIVAPKRGIRKHLQEWF\n+Mbo-CAD933 AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGSQSVPVTLRQAL\n+MtU-P96281 AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGSQSVPVTLRQAL\n+Mtu-P96281 AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGSQSVPVTLRQAL\n+Aga-SANGP0 VVGTVRTLWPGAKVEFND---VSANELNATVTTLD--LEDAEEIFLRLEKNGFLLLKYQL\n+Dme-Q9VK63 AMQPLRIVWP-EQFKLHC---TQLRGKLLKISALHPSLTAAASISLKHVVQLDAILKRDM\n+Sto-Q96ZY0 ---------------MNANTSTSPTSSL---LSTYINLGIIILTFVIPL--IFIYFMRMM\n+Sso-Q97V06 ---------------MATVTSNNSTIGLGLSSNTLQLVILTILFFLVPL--IWIYFSRRM\n+Aga-SANGP0 -----GICGVTQGPSVYGEVDRHTVIKI-DQILYHPA-----------------------\n+Sso-Q97W25 VL------------LMKIFGKSTAKFAYSDK-----------------------------\n+Hsa-IPI000 ALGSCCTAWPADGFAAVGASRSRRSLSL-NRLLLVPCLRRVAVWPVLRETAALEAAQELL\n+Fru-SINFRU LMGSCCTAWPAEGFSLMSHPPTQLQMDH-SKITPVTCLRCVKT-TVIVGSRLHELVKDML\n+Ath-C48B_A MLETESVCDNKWRA---------------------EA-----------------------\n+Cal-CA5106 ILSDSSAGVVSNDITISFPYRQLCGLLLGDRVELVKFPQYASDISISGVEDVSALIGLVY\n+Sce-AFG2_Y VLIGEGILVIDEEVTLSTTIRSVGNLILGDRLELKKAPPYATKVTVGSLLECEEKVIQKL\n+Spo-O60058 ALGEAGITQSGIGPLISPLLAKWANLKAFQRVNISQYLKEAEGIKIVASEPIESLIRKEL\n+Ana-Q8YUT8 ----------D---LFKG---FEQLIELVKTLEEKAEIKTDFQINSRSM-----------\n+Ecu-Q8SSJ5 TLKKALIFSTSVPPAIVRDGRFNLRIRITDTVKLYRVIPVVSKLNFLPIGNIDEFVRPFL\n+Pfa-MAL6P1 RMKRHTICIIDLDERINKVARKNLRVCLGDVVYVKSCIPYGKKIQVLPIDTLEIFLKPYF\n+Gth-Q98S05 KIKKKTVCIINCELRINKTVRENLNIGIGDIVTIHHFLKFGKRIHVLPFGNIEDFLKPYF\n+Ath-C48D_A TMKRKTVCIATCDERMNKVVRSNLRVRLGDVISVHQCVKYGNRVHILPLGNIDAYLKPYF\n+Ath-C48A_A TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPVGNLDAYLKPYF\n+Ath-C48E_A TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPVGNLDAYLKPYF\n+Cel-TER2_C KMKRRTVSIVNCPNKMNKVVRNNLRSRLGDVVSISSALEYGKRVHVLPIGNLDVFLRPYF\n+Cel-TER1_C KMKRKSVAIISCPNRMNRVVRNNLRIRLGDVVSITPALSYGTRIHVLPIGNLDVFLKPYF\n+Fru-SINFRU KMKRRTVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Rno-IPI002 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Mmu-IPI001 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Mmu-IPI003 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Hsa-IPI000 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Dme-Q9V3C3 KMRRKTVCIVTCPDRMNRVVRNNLCVHLSDVVSVQSCVKYGKRVRILPIGNLEIYLKPYF\n+Aga-SANGP0 KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPIGNLDVYLKPYF\n+Aga-SANGP0 KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPIGNLDVYLKPYF\n+Ncr-NCU000 TMKRKTVLIVDLDDRLNRVVRHNLRVKHGDIITIHPCIKYAKRIAVLPIGSLDVFLAPYF\n+Spo-CC48_S TMRRKTVLIVEMEDRINRVVRNNLRVRLGDIVTINPCIKYAERISVLPLGSLDVYLKPYF\n+Cal-CA3333 TMKRKTVLIVDMPDRVNRCVRNNLRVRLGDIVTVHPCIKYANRISVLPIGSLDLYLKPYF\n+Sce-CC48_Y TMKRKTVLIVELEDRINRVVRNNLRIRLGDLVTIHPCIKYATRISVLPIGNLDVFLKPYF\n+Hal-Q9HPU1 SMGRAARVWPDDGDRIDGRLRKEADVGIDDQVTVEPAIKPAGGVTVALPRGNAPMVRDRL\n+Hal-Q9HHW2 ALGRTARVWPDAGRRIDGQLRQAANVSIDDRVEVEKTVEPADRVTVSLPRGDGSHLREHL\n+Hal-CDCH_H TLETTAKVWRDWNTRIDGFTRQNAEVGIGERVKIRKAAEKADTLVLAPPGSDAGMVKR'..b'SPSLSITELKKYEMLRDQF\n+LPFTYTGADFYALEDISVMVTEQDFLDAHRELVPSVSAGELEHYEQVRAMF\n+CPPQLTGADLYSLGSSALMLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+CPPQLTGADLYSLGSSALMLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+CPPQLTGADLYSLRSSALLLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+CPPQLTGADLYSLRSSALLLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+RTDGFTGADLQALAGPQVVVNWKHLYKALDATRASISVKERKRLERIYHEF\n+GLDGYSAADCVALSIDAANVTAADLATARETVRASLDPLQVASLRKFTKGD\n+GLDGYSAADCVALSIDAANVTAADLATARETVRASLDPLQVASLRKFTKGD\n+GLDGYSAADCVALSIDAANVTAADLATARETVRASLDPLQVASLRKFTKGD\n+RTAGCSGSEIEAISFDVETIEWEHFEHALGVVRPRTSPELLRLYEEYLKQH\n+LTEGYSGAEIQAVSFEAEDVKWTDFEHALKAVPPRTSPELLKLYEDYLKRK\n+ITDGYTPADLKLVGVARTTLTFNDFIKILANVKPSVNKETLKMYEEFIQRI\n+LTENYTPADLKLVGNLRTEVKLEDFMDVLKRVKASLDRQTLIMYEKFFERR\n+QTERYSGADLQNLDLNATVVTMAHLRSALQDVRPSLTKEQIDWYHSYANRL\n+QTEGYSGADLAALGESNRTLTREDLIDALNKIHPSVKKRLSKGSSSNDHET\n+ETCFFSGADLRNLGLDATTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKE\n+KTELYSGADLQNLNLEASALKHRYFVQALSRMRPSLTEQQINSYQ------\n+ETDLFTGAELEGLNIAATAVFNRHFQTAKSSLKPALTIEEVETYSSFRKAA\n+LTDGCSGAEVTLLNKEATTVTNKHFEHALKGISRGITPEMLEYYEKFSKKS\n+RTEGYSGAEVVLLDLDVAKVELRHFEKAFKGIARGITPEMLSYYEEFALRS\n+KTEGCSGAEVVALDLEAKEICQAHFKTALLALRKAITRDMLEYYASFSESV\n+MTQDWNGADLTLLDPSEIKITTDDFNYAYKVLTEQRPD-------------\n+ATDKFSGADLSEIEDPVPYLRPDHLVQSLKTARRSVSEKEVERYEAFARSM\n+KTAGFSGADLAELDDDNIEITRHHFKEGLAGARRSVSQADLIKYDNFRIKF\n+ATSGFSGADITEIIDPVPEITKEHFLEAMKYARRSVSDSDIRKYEMFAQKL\n+YTQGFSGADITEIDEEEIEIKAGHFEESMKYARRSVSDADIRKYQAFAQTL\n+YTQGFSGADITEIVDEVSEIKAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+YTQGFSGADITEIDDEVSEIRAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+NTVGFSGADLTEIADPVPEITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+NTVGFSGADLTEIVDPVPEITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRKDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSVADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+VTQGFSGADLTEIDDPVPEITSAHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+VTQGFSGADLTEIEDPVPEITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+VTQGFSGADLTEIEDPVPEITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+KTHGFSGADLGFIEDPVPELTKRHFEEAMSMARRSVSDVEIRRYEAFSQQM\n+ATHGFSGADLEFVDEDASQVQRHHVEEAMKMARRSVSDAEVRRYEAYAHQL\n+ITHGFSGADLSYIEDPVPYITRAHFEEAMKTAKRSVSDAELRRYESYAQQL\n+ATQGFSGADLLYIVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM\n+RMDGFVGADVEALSVGNVRVTMAHFEAALGEVTASVDADVKENYEEIEQRF\n+RTDGYVGADIEAVNVDEIELSIEHFEQALEEVDSN-AGSETQAFEKPAEAV\n+RADGYVGSDLANIDEDADDVGMAHFRAAMENVRPTITDDLMEYYDQVEDQF\n+LTDQYTGADIAAVDLHAKSVRQKHFLQAIEETGPSVTPDTMKYYQAIRGEL\n+FTDQYTGADIAAVDLHAKKVRQKHFLQAIEETGPSVTPDTMKYYEAIKGEL\n+RTEGYVGADLENLNPDATSVSQKNFLDALKTIRPSVDEEVIKFYRTLSETM\n+RTEGYVGADLENLNPDATQVSQKNFIDALKTIRPSIDEEVIKFYKSISETM\n+RTEGYTGADIAALTVKAKPVSMKHFEEALKRIPPSLTPEDIRRYEEIAKRL\n+MTEGYTGADIEAVKLEVGKVEMRHFLEALKKVPPSLTKEDILRYERLAKEL\n+KLEGYTGADIEALSNLEIKITMQDFLDTMKIVTPSLTKADIMRYENMVKEI\n+KTEGYTGADIEALNNAKVIVTKEDFNKALEVVKPSLTAADIQRYERLAKEL\n+RTEGYSGADLELLDINAKEVSMRHFEEAMKKVRPSITPDMLKFYESWLEKA\n+RTEGYTGADIEALDINAAEVSMRHFEVALKKVKPSVTPQMVEYYKRWLETV\n+KTEGYTGADLAALKVNGVKVSLRHFEEAMRKVKPSVTQDMLQFYQNWVEKA\n+KTEGYTGADLAALKGKGVLVEKRHFDIALKKVRPSVTMDMIQFYQNWLEKA\n+RTEGYTGADIAAVIRRLAKVTMKDFEEALRKIGPSVSKETMEYYRKIQEQF\n+RTEGYTGADIAAVIKQKAKVTMKDFEEALKKIGPSVSKETMEYYRKIQEQF\n+KTEGYVGADIEAVNMDAEEVSMKYFLEAMEKVKPKGGVEEQVQYH------\n+KTEGYTGADIEALRLKVSKIKKEHFMKALEKIKPSVSKEDMRVYEKLAQEY\n+KTEGYSGADIEAVAAKKLKITKKHFEEALKKVRPSLTKEDVEKYEKLIEDF\n+MTEGYVGADIEGIKAAEVRLSKRHFEKAIRRVKPTTSRETLSAYEKSAELF\n+MTEGYVGADIEGIKAGDVRLSKRHFERAIRRVRPTTSRETLSAYEKSAELF\n+KCNNFSGADLAALSGEEIIVTMSDFRSALRKIKPSVSDKDRLKYDRLNKKM\n+RCSNFSGADLAALALEPIRVTNADFELAFKNIKPSVSDRDRQKYQRLAKRW\n+NCEGFSGADLAHLDITQCTIKTRHFEQALSLVSPSVNKQQRRHYDALSTKL\n+RCENFSGADLEALGSYPRRTKMVHFEEASSRMQSGR---------------\n+KTAGFSGADLQGLSTSAAVVTINDLLEACQETKPSISTSELVKLRGIYDRF\n+KTTGFSGADMQGLNKSKVLITHENFLESLKETKPSISHSEKIKLTKIYKEF\n+VTDSFTGADLKALNQPGPAISQSHLMTALGHTRPSISEDDWKNFAELYESF\n+ATEQFTGADLKALLRPGLLLSAAHLNAALAVTRPSLSRDDWNRYTNLYEAF\n+MTEGFSGADLQALTGTTPIITDPLLKSIASKTKPSVSETEKQKLYDIYSQF\n+KTANYTGADIQSILAKKISLKQKHLIESFQTTRPSLSASDVAKYHRTYARF\n+KSEYYTGADIRSIVPEQITVSQRHLAEAFSSTRPSLSPRDIAKYRETYARF\n+\n+\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.012.AA.SuperAlignment.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.012.AA.SuperAlignment.phy Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,38803 @@\n+ 22 101184\n+Cgl --MD-----------------------------------LLGDIVEKDVDEVSEVGELPD\n+Kla --MD-----------------------------------LFGDIVERETV-APDAVSNQG\n+Sba --MD-----------------------------------LLGDIVEKDTF-NAVESNDND\n+Sca --MD-----------------------------------LLGDIVEKDPS-SSTSSANAS\n+Sce --MD-----------------------------------LLGDIVEKDTSDSVESNDNGT\n+Sku --MN-----------------------------------LLGDIVEKDTS-VENNDNDSL\n+Smi --MD-----------------------------------LLGDIVEKDTSDSVESNENDL\n+Spa --MD-----------------------------------LLGDIVEKDTSDSVENNDNDA\n+Zro --K---------------------------------------------------------\n+Ago --MD-----------------------------------VVGEIVERETA-PAEAPAPDG\n+Skl --MD-----------------------------------LLGDIVEKETVEIQEAPAAPS\n+Cal --MD-----------------------------------FIGEIIEHETE-APKEPTPK-\n+Kwa --MD-----------------------------------LLGDIVEKDVSQGPALESAPA\n+Dha --MD-----------------------------------MLGEIVEHEIE-APKPPQM--\n+Cdu -MMD-----------------------------------FIGEIIEHETE-TPKEPTPK-\n+Lel --MD-----------------------------------FVGEIIEHEIEEPTAPLAPTT\n+Ctr --M---------------------------------------------------------\n+Clu --MD-----------------------------------LIGEIVEHDVA-VASPPEPSI\n+Pst --MD-----------------------------------FIGEIVEHEIEAPSLTID---\n+Cgu --MN-----------------------------------LIGEIVEKEIE-PPAEFKAS-\n+Kpo --MD-----------------------------------LLGDIVEKDVEETPTAEISEN\n+Yli --MD------------------------------------VGDIIERDIEDTPAP-----\n+\n+----------------GG--------------FPKL--YKPEKVS-SWKARLKRKQQ---\n+-------------MPTTG--------------FPKL--HQPEKVS-SWKQRLMEKKK---\n+APIAN--------NSKTG--------------FPEL--YRPKKIS-SWKERLREKRA---\n+ASTSNQQSSYPSSSATTG--------------FPEL--YKPSKIS-SWKHRLKAKKQ---\n+LSTN---------NCGTG--------------FPEL--YKPKKIS-SWKERLREKRA---\n+MSN----------NSKTG--------------FPEL--YKPKKIS-SWKERLREKRA---\n+LISN---------NSKTG--------------FPEL--YKPKKIS-SWKERLREKRT---\n+LITN---------NSRTG--------------FPEL--YKPKKIS-SWKERLREKRA---\n+------------------------------------------------------------\n+-------------VQPRG--------------FPEL--YRPAAIS-SWRQRLQKKNG---\n+----------------SG--------------FPEL--YQPEKIS-SWKVRLQEKKR---\n+-------------PTIGG--------------FPELKKLKEKKVS-RWRQKQQQEQS---\n+----------------TG--------------FPAL--YEPEKVS-SWKVRLQQKRR---\n+-------------TAKTG--------------FPDLNKLKEKKVS-KWKQRLESKKV---\n+-------------PTLGG--------------FPELKKLKEKKVS-RWKQKQQQ------\n+QGSD---------LLNTG--------------FPDPLNHKKRYNS-RWTMKRGAKPA---\n+-------------KTENG------------------------------------------\n+-------------SSSSG--------------FPTLKKFGGKRTS-----RFKKQTD---\n+-------------VEVGG--------------FPDPSKSREKKVS-RWKKRVQKKGT---\n+-------------DITSG--------------FPAADLLKKKRAS-KFKSAQKANIT---\n+TRE----------LSKNG--------------FPEL--YKPEKIS-SWKQRLRAKAA---\n+--------------------------------LPPMPPKAPSAFKREWKRKPKPAPA---\n+\n+-----------------------ASQTGKVNELSSSRES---------------------\n+---------------------KKQQRSNTGSEPPNANFV-------------------EV\n+-----------------------QRKDSGAKETKKQQVA---------------------\n+-----------------------QQQQQEQRPATRASPR---------------------\n+-----------------------QKKKTSGKDAEKQQTS---------------------\n+-----------------------RQRRTSANEAKKQQST---------------------\n+-----------------------QKKKSSAKDAENEQVA---------------------\n+------------------------QKKTGAKQTEKQQAT---------------------\n+------------------------------------------------------------\n+-----------------------QRRPPAAALAA--------------------------\n+-------------------RGLKHKKQQATDPEPRAEQA---------------------\n+------------------------------TTSPKTTEI---------------------\n+-----------------------NRAASARTVKPVEKKN---------------------\n+---------------------------PEVQQSNPVTTE---------------------\n+-----------------------EQQQKTASHKPTETRS---------------------\n+-----------TSKVDDV'..b'------\n+WLIDLLVYLNQELLQLIYVKNNFLNSIVLPLILNKVSRLFLMYAISAMGRTHEILKKLHK\n+WFVKLVTFLTQQMIVLINKPEDQENTLVLGILSSKMTRQLLLSVLSEIRKIIHLVTKFPE\n+------------------------------------------------------------\n+WLIDLLVYLNQELLQLIYVKNKFLNSIVLPLILNKVSRLFLMYAISAMGRTHEILKKLHK\n+WLIDLMAYFNQELMQLTYFKNDSRSSIVLPVILSKVPRLFLMYAISSMGKTHEILKKLHK\n+WLIDLLAYLNQELLQLTYMKNSNLSSLAIPIIMGKVPRLFLVYAITSMGRTHEILKKLHK\n+WLIDLIVYLNQELLQISLSKDNPDNSVTLPLIMSKVPRLFLMYAISSIAKTHEILKKIHK\n+------------------------------------------------------------\n+WLIDLIIYLNQEFNQLANSKGDPSISVVLPIVLSKVPRLFLMYALSSIQKTHETLKKLHK\n+WIVKFVTCLVQDLLILINNPGINDSKLVYGVLGARIPRALILSILTEIKRVTQLITKFPE\n+WCLDFAAYLCQELLAASNEGPSYFQHVALPMVMARSSRMLLMYSWRGIRSLDTILMQKPG\n+\n+TNYPILNESSTYLKMLLIESPINFEKFETFLMDVNNKLSAFSEQQPSIMREPTLLVRSVP\n+IAFPILNESSQFFRKVINDCTVNLDLFETFLSEFGSKINELDQNTVQQKYEAEFLIKTVP\n+NSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALSEQQPSQEREFSLLVKAIP\n+NSYPILNESSHFLKLVLDDSPVNFEKFETFLVDVNNKFTTFSEQQPSQGREPSLLVNAIP\n+TSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALCEQQPSQEREFSLLVKAIP\n+TSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALCEQQPSQEREFSLLVKAIP\n+------------------------------------------------------------\n+TSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALCEQQPSQEREFSLLVKAIP\n+------------------------------------------------------------\n+TTYTVLNESSRFLRKALGDSPVNLEKFEVFLNEINNKFLSLLDDHGSMDREPSFMVKAIP\n+------------------------------------------------------------\n+DLFAPMKESLNRYFSISNNSPITVNLFESYLRECDALLNKEVPQKIALKFEQKLLIKGIS\n+TTFPILNESSIYLRKVLSDSPVNFEKFETFLADVNYKFTSLSEQQTSTIKDSYLIIDGIP\n+------------------------------------------------------------\n+DLFAPMKESLNRYFSISNNSPITVNLFENYLRECDALLNKEVPQKIALKFEQKLLIKGIS\n+DLFKPMKESLNRYFTIFNNAPLTLNLFENYLRECDALVTKEMATKGSLKIEQSLVFGIIP\n+DLFTPMKESLNRYFSIYNTAPITVNLFENFLRECDALCTKELSAKFALRCEQKLVCQGLP\n+DLFTPMQEALMRFFGTCGSSPLNLNVFENFLRDCDTSTSKDLAARAPLQLEHQLFCIGIP\n+------------------------------------------------------------\n+DLFQPMKEALNRYFTTCANSPLQISLFESFLRDTDAVIAKEISQNPQLRVEQKLVFQGIS\n+NTFPVLNESSAFLKMILNESPVSFERFETFMIDINNKFSSLNEQEPSTKREPSLLVKAIP\n+TETQEAGLASQRQRELSHFTPISMTFFEQLFNVIDSHTKQVAENVERLGLEQQLLFQGIP\n+\n+NELNKITEFLLQYSSNVISHADASAIYFSDTSGLRISCDTYDRFSLSLKRCNRCGAVTIP\n+DSLPEFDSILRATTMSLLPNINLSTVFFTDTSFLNLCWETSEHVDRSIKKCCRCGTFTVD\n+PEFSKVGDFLLQYANNVISHANAAAVYFADTSGLKISNTTCDKLSISLKRCSRCGSVTIS\n+LDSIKMYDFLLTYSNNVISHVDAAEIYFCDTSGLRISNMTCDQLSLSLKRCRRCGSVTVG\n+PEYAKVGDFLLQYANNVISHANAAAVYFADTSGLKISNSTCDKLSISLKRCSRCGSVTIS\n+LEYAKVGDFLLQYANNVISHANAAAVYFADTSGLKISNTTCDKLSISLKRCSRCGSVTIS\n+------------------------------------------------------------\n+PEYAKVGDFLLQYANNVISHANAAAVYFADTSGLKISNSTCDKLSISLKRCSRCGSVTIS\n+------------------------------------------------------------\n+PALGHVREFLLSFAGSLLAQTNLAEVFFASTHNLRIFDHSSEWVDLVIKRCVRCGCVTVA\n+------------------------------------------------------------\n+NTIIELSNMILDRYSIISRETKLSELMFYDTDWLNIGINSDSSTSAKLRVCTRCRAVSLV\n+EQVSHLKDFLLSYSNTVISHIRPAEVYFSDTRGLRIFASSKEAISEKLKRCCRCGAVTVS\n+------------------------------------------------------------\n+NTIIELSNMILDRYSIISRETKLSELMFYDTDWLNIGINSDSPASPKLRVCTRCRAVSLV\n+SEVQDLAKTLVERYSIIARESKVPDLFFYDTEWLNLGNEGVDALRIFVRRCTRCRSVSLV\n+DEFIEVAQILLDRFTLSSREIKVAELISYPTEWLDIGVMYDEGEDLKLRQCTRCRAISSV\n+SPLISVAITMTDHHYAISRDSKLSELFFYNTDWIDAGVGGVSTMGVSIRKCTRCRAVSLI\n+------------------------------------------------------------\n+EEYIPIATAVVGKYANISLDMKVSELFFYDVDWIGVGIQLRKVVIKGVRKCTRCRSVSLV\n+PEYTKICDFILTCTKSILSHIDPAFVYFTDTSGLGISKESYDTFTLNLKRCCRCGCITIS\n+QQFLPLAKRCVDEFDKFRKTNDLSPLYFYNVSWLGLDEHCLRKFIQELRVCQRCAGTSVF\n+\n+TNKTRRWPTMYTRMCICLGMLYEL\n+GQNTKRWTALYYRNCHCTGLLYEI\n+GDKTKRWPTMYTRLCICSGMLFEM\n+KNKTRRWPTMYTRNCICSGMLYEL\n+SDKTKRWPTMYTRLCICSGMLFEM\n+SGKTKRWPTMYTRLCICSGMLFEM\n+------------------------\n+SDKTKRWPTMYTRLCICSGMLFEM\n+------------------------\n+KNNTKRWTALYSRYCQCTGLLYEL\n+------------------------\n+GDVTGLWTMVFQRTCMCGNAWVNV\n+KDNTKRWTSLYSKICICSGFLYEL\n+------------------------\n+GDVTGLWTMVFQRTCMCGNPWVNV\n+TDPLGLWTMVFQRTCICGNAWVNE\n+TDISGLWTMLFQRNCNCGNPWITN\n+ADPLSLWTMVFQRTCICGSAWVNC\n+------------------------\n+NDPLGLWTMVFQRSCICGSIWINT\n+GDKTKRWPTMYARVCICSGYLYEL\n+VDSSTHWTFAFQRNCWCGGMWIPE\n+\n+\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.013.AA.SuperAlignment.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.013.AA.SuperAlignment.phy Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,21346 @@\n+ 22 55653\n+Cgl MDLLGDIVEKDVDVSEVGELPD---GGFPKLYKPEKVSSWKARLKRKQQASQTGKVNELS\n+Kla MDLFGDIVERETVAPDAVSNQGMPTTGFPKLHQPEKVSSWKQRLMEKKKQQRSNTGSEPP\n+Sba MDLLGDIVEKDTFNAVESNDNDNSKTGFPELYRPKKISSWKERLREKRAQRKDSGAKETK\n+Sca MDLLGDIVEKDPSSSTSSANASSATTGFPELYKPSKISSWKHRLKAKKQQQQQQEQRPAT\n+Sce MDLLGDIVEKDTSSVESNDNGTNCGTGFPELYKPKKISSWKERLREKRAQKKKTSGKDAE\n+Sku MNLLGDIVEKDTSVENNDNDSLNSKTGFPELYKPKKISSWKERLREKRARQRRTSANEAK\n+Smi MDLLGDIVEKDTSSVESNENDLNSKTGFPELYKPKKISSWKERLREKRTQKKKSSAKDAE\n+Spa MDLLGDIVEKDTSSVENNDNDANSRTGFPELYKPKKISSWKERLREKRA-QKKTGAKQTE\n+Zro K-----------------------------------------------------------\n+Ago MDVVGEIVERETAPAEAPAPDGVQPRGFPELYRPAAISSWRQRLQKKNGQRRPPAAALAA\n+Skl MDLLGDIVEKETVIQEAPAAPS---SGFPELYQPEKISSWKVRLQEKKRHKKQQATDPEP\n+Cal MDFIGEIIEHETEAPKEPTPK-PTIGGFPELLKEKKVSRWRQKQQQEQS-------TTSP\n+Kwa MDLLGDIVEKDVSGPALESAPA---TGFPALYEPEKVSSWKVRLQQKRRNRAASARTVKP\n+Dha MDMLGEIVEHEIEAPKPPQM--TAKTGFPDLLKEKKVSKWKQRLESKKV----PEVQQSN\n+Cdu MDFIGEIIEHETETPKEPTPK-PTLGGFPELLKEKKVSRWKQKQQQ---EQQQKTASHKP\n+Lel MDFVGEIIEHEIEPTAPLAPTTLLNTGFPDPHKKRYNSRWTMKRGAKPASKGNTTATTTT\n+Ctr M---------------------KTENG---------------------------------\n+Clu MDLIGEIVEHDVAVASPPEPSISSSSGFPTLFGGKRTS----RFKKQTDPVKDQLEKKKN\n+Pst MDFIGEIVEHEIEPSLTID---VEVGGFPDPSREKKVSRWKKRVQKKGTDAAKPLRESAN\n+Cgu MNLIGEIVEKEIEPPAEFKAS-DITSGFPAALKKKRASKFKSAQKANIT-KAPNNQNDTK\n+Kpo MDLLGDIVEKDVETPTAEISENLSKNGFPELYKPEKISSWKQRLRAKAARSGEDNSNERV\n+Yli MD-VGDIIERDIETPAP----------LPPMKAPSAFKEWKRKPKPAPAPAPAPVNNQAP\n+\n+SSRESRAVEESAAQRIHRENLETMRKMSPEEIARERQELLESLDPKLIQKLLKNV-----\n+NANFVDPNALSEAERIHLQNLAVLQSMTPEQFERERQELMDSLNPNVLKSLIARVKKMTR\n+KQQVATDAPLSEAKSIHEENIKVLQEMTDDQIISERQDLYDSLDPKLIASLLKNINKRAK\n+RASPR--QKTSEAQSIHNENLNTLQNMTDEQIINEQRELLQSLNPKLIKNLLANINKRTE\n+KQQTSTDAPLSEAKSIHNENIKVLQGMSDEQIVQEREDLYNSLDPKLIAKLLKNINKRAK\n+KQQSTTEAPLSEAKSIHNENIKVLQEMTDEQIMQERQDLYGSLDPKLIAKLLKNINKRAK\n+NEQVATDVPVSEARSIHNENIKLLQEMTDEQIIQERKDLYDSLDPKLVTKLLKNINKRAK\n+KQQATTDAPLSEAKSIHNENIKILQGMTDEQIAQERQDLFDSLDPGLIAKLLKNINKRAK\n+----------------------------------------------LVQKLIRNMEKRA-\n+----------SEAEKIHKENMAYIEGLSEEQRTAERRELLESLDPKVVQALYRRLDARAA\n+RAEQAPDSTMSEAERIHLENIKLMMEMSPEQLEREKQELLDSLDAGVIQGLLKRIGKKQM\n+KTTEI----RSEASKIHQENIEKMAQMSEEEILQEREELLKGLDPKLIESLIGRSKKRED\n+VEKKNSKGAESEAERIHNENVARMQQMSPQQLENERRELLESLDPKVLHALLKRAAKNDS\n+PVTTE---PKSEAEKIHQENLDKISQMTSEEIEQEQAELLSGLDPNLIKSLLKRSEKKEN\n+TETRS------EASKIHQENIEKMAQMSEEEILQEREELLKGLDPKLIESLIGRSKKREG\n+STTTTQTEPVSEAEQINQENIAKLNLMTDAEIMAERESILKQLNPKLVQSLIQRLQKRDE\n+---------LTDLSQLDKEDVDRALRITSNDFENDQRDRKVKFDDNIK-------TVND-\n+EEKEA---ELSEAEKINRENLEKLSKMSEGEIEQERRELLEGLDPKLISSLLKRA-----\n+KVKNKVVNDLTEAEKIHQENMDKIASMTEEEITHEREELLQGLDPKLIQSLLKRTESRIS\n+PTKNT-----SEAQKIHQENLDKIASMTDAEIMQEQQELLSGLDPNLVKNLLKRSTARSK\n+RAKPANEEKRTEAQSIHMENLNTINNMSDEQIMQEKRELFESMNPKLIQKLLANINKRSK\n+PAKPTSDQKLTEAEEIHLENLSKLAKMSPEEIEAQRQEIMESMDENVLMALMRRAKIKET\n+\n+-QKSDKIFAEIEGASGTWVGGKNEAVADLPPLDEDMVNRALDLNATELPKETSASLPKDD\n+SKPPVPQYAEIE-GPGTWIGGSNKVK-DLPKLDDKAVDEALGIN--SVEVQPLKSVRFER\n+DETNTPLFAEIEGASGTWVGGNKQGINNLPSLEDDDVNAALDIR--PKSSTNTKHVVFEE\n+GESSAPLFAEIEGASGTWVGGKNENFKHLPSLSDDQVNKALDIQDEDLPTVEAHTEKEQD\n+DENNTPLFAEIEGASGTWVGGNKQGIYDLPPLDDEDVDVALEIR--PMLGKDAKHVQFEE\n+EENNAPLFAEIEGAPGTWVGGNKQGIYDLPALEDEDVNAALEVR--PQSSINSTHVQFQE\n+DENNTPLFAEIEGASGTWVGGNKQGIYDLPPLEDEDVNAALDIR------PNSKHVKFDE\n+DENNAPLFAEIEGASGTWVGGNKQGIYDLPPLEDEDVNAALEIK--PKSGINPKHVQFEE\n+SENQQTLFPEVEGAPGTWVGGNRENG-ELPSSSDEQVDKASGIQ--SNSKPKEKSVSFAE\n+ADGTAPLVAEVEGAAGTWVGGTREEP-MMPRLDDATVDAAL---GAPQASMPEAAPTYDL\n+SSATTPLFAEIEGAPGTWVGGSREFP-DLPRLDDDAVDKALGIV--KKPAEEAKHVKFIE\n+HEHNGHAHEHAE-GYHGWIGSMKTSEGDLSQLDKEDVDRALGISSEPEGGSNTKKVAFDD\n+KPTAAPLFAEIDGAPGTWIGGSHDIP-DLPRLDDAAVDRALGIP-----ETPSKHVNFKC\n+DGHDEHVHAE---GFNGWIGGGRTSDEDVTLLDEKDVDKALGISQDNEPKDNSKTVRFED\n+HGHNGHTHEHAE-GYHGWIGSMKTSEGDLSQLDKEDVDRALGISESDGNNNSTKKVTFDD\n+GSDHTHRHQHAE-GYNGWI'..b'IGNFKWLIDLLVYLNQELLQLIYVKNKFLNSIVLPLILNKVSRLFLMYAISAMGRT\n+ILSLIGNIKWLIDLMAYFNQELMQLTYFKNDSRSSIVLPVILSKVPRLFLMYAISSMGKT\n+IISLLGSFKWLIDLLAYLNQELLQLTYMKNSNLSSLAIPIIMGKVPRLFLVYAITSMGRT\n+IVSLVGSVKWLIDLIVYLNQELLQISLSKDNPDNSVTLPLIMSKVPRLFLMYAISSIAKT\n+------------------------------------------------------------\n+IVSLIGSVRWLIDLIIYLNQEFNQLANSKGDPSISVVLPIVLSKVPRLFLMYALSSIQKT\n+VHSLIPIAKWIVKFVTCLVQDLLILINNPGINDSKLVYGVLGARIPRALILSILTEIKRV\n+LMSLSGLKRWCLDFAAYLCQELLAASNEGPSYFQHVALPMVMARSSRMLLMYSWRGIRSL\n+\n+TAIITKFPETNYPILNESSTYLKMLLIESPINFEKFETFLMDVNNKLSAFSEQQPSIMRE\n+ANLMIKFPEIAFPILNESSQFFRKVINDCTVNLDLFETFLSEFGSKINELDQNTVQQKYE\n+TQIVAKFPENSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALSEQQPSQERE\n+IQIISKFPENSYPILNESSHFLKLVLDDSPVNFEKFETFLVDVNNKFTTFSEQQPSQGRE\n+TQIVAKFPETSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALCEQQPSQERE\n+TQIVAKFPETSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALCEQQPSQERE\n+------------------------------------------------------------\n+TQIVAKFPETSYPILNESSTFLKLVLSESPVDFEKFETFLVDVNNKFIALCEQQPSQERE\n+------------------------------------------------------------\n+IGLITKFPETTYTVLNESSRFLRKALGDSPVNLEKFEVFLNEINNKFLSLLDDHGSMDRE\n+------------------------------------------------------------\n+HEILKKLHKDLFAPMKESLNRYFSISNNSPITVNLFESYLRECDALLNKEVPQKIALKFE\n+IHLVTKFPETTFPILNESSIYLRKVLSDSPVNFEKFETFLADVNYKFTSLSEQQTSTIKD\n+------------------------------------------------------------\n+HEILKKLHKDLFAPMKESLNRYFSISNNSPITVNLFENYLRECDALLNKEVPQKIALKFE\n+HEILKKLHKDLFKPMKESLNRYFTIFNNAPLTLNLFENYLRECDALVTKEMATKGSLKIE\n+HEILKKLHKDLFTPMKESLNRYFSIYNTAPITVNLFENFLRECDALCTKELSAKFALRCE\n+HEILKKIHKDLFTPMQEALMRFFGTCGSSPLNLNVFENFLRDCDTSTSKDLAARAPLQLE\n+------------------------------------------------------------\n+HETLKKLHKDLFQPMKEALNRYFTTCANSPLQISLFESFLRDTDAVIAKEISQNPQLRVE\n+TQLITKFPENTFPVLNESSAFLKMILNESPVSFERFETFMIDINNKFSSLNEQEPSTKRE\n+DTILMQKPGTETQEAGLASQRQRELSHFTPISMTFFEQLFNVIDSHTKQVAENVERLGLE\n+\n+PTLLVRSVPNELNKITEFLLQYSSNVISHADASAIYFSDTSGLRISCDTYDRFSLSLKRC\n+AEFLIKTVPDSLPEFDSILRATTMSLLPNINLSTVFFTDTSFLNLCWETSEHVDRSIKKC\n+FSLLVKAIPPEFSKVGDFLLQYANNVISHANAAAVYFADTSGLKISNTTCDKLSISLKRC\n+PSLLVNAIPLDSIKMYDFLLTYSNNVISHVDAAEIYFCDTSGLRISNMTCDQLSLSLKRC\n+FSLLVKAIPPEYAKVGDFLLQYANNVISHANAAAVYFADTSGLKISNSTCDKLSISLKRC\n+FSLLVKAIPLEYAKVGDFLLQYANNVISHANAAAVYFADTSGLKISNTTCDKLSISLKRC\n+------------------------------------------------------------\n+FSLLVKAIPPEYAKVGDFLLQYANNVISHANAAAVYFADTSGLKISNSTCDKLSISLKRC\n+------------------------------------------------------------\n+PSFMVKAIPPALGHVREFLLSFAGSLLAQTNLAEVFFASTHNLRIFDHSSEWVDLVIKRC\n+------------------------------------------------------------\n+QKLLIKGISNTIIELSNMILDRYSIISRETKLSELMFYDTDWLNIGINSDSSTSAKLRVC\n+SYLIIDGIPEQVSHLKDFLLSYSNTVISHIRPAEVYFSDTRGLRIFASSKEAISEKLKRC\n+------------------------------------------------------------\n+QKLLIKGISNTIIELSNMILDRYSIISRETKLSELMFYDTDWLNIGINSDSPASPKLRVC\n+QSLVFGIIPSEVQDLAKTLVERYSIIARESKVPDLFFYDTEWLNLGNEGVDALRIFVRRC\n+QKLVCQGLPDEFIEVAQILLDRFTLSSREIKVAELISYPTEWLDIGVMYDEGEDLKLRQC\n+HQLFCIGIPSPLISVAITMTDHHYAISRDSKLSELFFYNTDWIDAGVGGVSTMGVSIRKC\n+------------------------------------------------------------\n+QKLVFQGISEEYIPIATAVVGKYANISLDMKVSELFFYDVDWIGVGIQLRKVVIKGVRKC\n+PSLLVKAIPPEYTKICDFILTCTKSILSHIDPAFVYFTDTSGLGISKESYDTFTLNLKRC\n+QQLLFQGIPQQFLPLAKRCVDEFDKFRKTNDLSPLYFYNVSWLGLDEHCLRKFIQELRVC\n+\n+NRCGAVTIPTNKTRRWPTMYTRMCICLGMLYEL\n+CRCGTFTVDGQNTKRWTALYYRNCHCTGLLYEI\n+SRCGSVTISGDKTKRWPTMYTRLCICSGMLFEM\n+RRCGSVTVGKNKTRRWPTMYTRNCICSGMLYEL\n+SRCGSVTISSDKTKRWPTMYTRLCICSGMLFEM\n+SRCGSVTISSGKTKRWPTMYTRLCICSGMLFEM\n+---------------------------------\n+SRCGSVTISSDKTKRWPTMYTRLCICSGMLFEM\n+---------------------------------\n+VRCGCVTVAKNNTKRWTALYSRYCQCTGLLYEL\n+---------------------------------\n+TRCRAVSLVGDVTGLWTMVFQRTCMCGNAWVNV\n+CRCGAVTVSKDNTKRWTSLYSKICICSGFLYEL\n+---------------------------------\n+TRCRAVSLVGDVTGLWTMVFQRTCMCGNPWVNV\n+TRCRSVSLVTDPLGLWTMVFQRTCICGNAWVNE\n+TRCRAISSVTDISGLWTMLFQRNCNCGNPWITN\n+TRCRAVSLIADPLSLWTMVFQRTCICGSAWVNC\n+---------------------------------\n+TRCRSVSLVNDPLGLWTMVFQRSCICGSIWINT\n+CRCGCITISGDKTKRWPTMYARVCICSGYLYEL\n+QRCAGTSVFVDSSTHWTFAFQRNCWCGGMWIPE\n+\n+\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.014.AA.EggNOG.COG0591.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.014.AA.EggNOG.COG0591.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,440709 @@\n+>177437.HRM\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-----------------------------------------------------------M\n+N-PYQL---------------FLC-----------------LL-----------------\n+-FAY-----TAL----------------LIS-------VGWYF-NKR---------QQ--\n+T-----------------------------------------------------------\n+--------------------QTDF---FL---AG----K--NA--G-------M---LSI\n+-----G-CSA-A-----------ASW-LTAG---G---ILA------VIG-F----F---\n+-------------------M-L--LGM--G---SV-W----G-FV----A----PNII--\n+-A------LFA-------IGLFV--RKI-K-G------L----------------P--AI\n+TQPE---LL-----------------------------E-------------LRY-----\n+----------GS---Y---------L-----RL-PV--A-IIITV---VM---I--LF-A\n+V-----------A-DI--KGF---------------------A-M---------------\n+-----------------VLS-----T---F---Y--------------------------\n+------------G------V--S------------PLM-SALI-V--ALAVS---I--YV\n+-TM-----GGLSAVIA--T-D---------IIQF--LCLTLF--VLI-M-A--GVV----\n+--M--TS---A-GTL-------------TA---------EPV----A---------ALLT\n+--SV-PD-----------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+NW---------------W-N---P--------GS--IG----------------------\n+-------------LP---------------------------------------------\n+------M-IL--IFS---------IA----I--------------IP------G-WITE-\n+---QD---QW-QKVW------AAT-D-E-RS-A----RN---------GM-FLG------\n+-----SV--LVTV---------V-FAGCA-F--------L----ALGLN-----------\n+T-----------------------------------------------------------\n+------------------------------------------------------------\n+-------------IY----------------PEIAGAG----------------------\n+--F---PM-GMAR---AEP-A--L---LT----------FI-M--D----H-----N---\n+-F-S-GF----------ILALS-AVGLATA----A---M---------------------\n+-------------S-CTDT--FATSGASCI--------SRDIFQRYL----H--------\n+------------------------------------------------------------\n+----------------PG-A----T-MKQM--LV-------------VNR-----IS---\n+------------V-VIII-VF--AT-----------L-GS-------F--FI---G--'..b'-\n+------------------------------------------------------T-----\n+--L---E--NPET---VFL-V--L---SQV----LF-H------------P-----F---\n+-V-A---------------GLV-LAAVLAA----I---M---------------------\n+-------------S-TISS--QLVVSSSAL--------VEDLVKMTG-----R-----E-\n+------------------------------------------------------------\n+------------------------MSARVQ---------------VMLGR-----AAV--\n+--------------LLVA-IV--AG-----------L-IA-------------LDR----\n+-SS---------------TILDLVG--FA----------------WAGFGA--AFG-P--\n+----------------------------------------IV---L--------------\n+----------------------LSLYW--------RR-----L-TR-----------W--\n+-G--ALA--GM----V-------TGA-------VV-AF--A------------------W\n+GQ---S-----------------A------------------------------------\n+---LS-------------------------------------------------------\n+------------------------------------------------------------\n+----------------DTLY-------EIVPG--FV---LG-----------------G-\n+LV-A---------I-LV----------S-L---AS-PR-P--A-----------------\n+-------------------------DDIGEE------FD----------DARRFTRG---\n+----------------QTEDP----------------------TPTVA------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,239148 @@\n+>860228.Ccan_20130\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------M-GLKIK------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------KM----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M-RR--LL--------------------FL----\n+-LL--------------------------------NL-------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------IVCG\n+FSFAQ-EKK-----------------------------------------\n+--------------------------------------------------\n+-------------------------V---TGVV-----------------\n+--KD---ET-------GV--PL-PGVT--IL--VQ---------GEK---\n+--A--------T-GT-Q------TDF-EGNYSIKVA-------------V\n+G---------------KT---LEFSYIGLT-TVTK---KVG---------\n+V-S--N---------------------------K---I------DVV--L\n+-R--E--D-TQQ-LS----EV--VI----T--GIT-T-TD-RR--LFTGA\n+SDKL-S-A-V---DIK--V--D--G-V-V-DVSRALEGRSSGVTVQ-NV-\n+----S-----G-AFGA---------AP--KIRVRG-A-TSIY--------\n+-------GG-SK--------------------------------------\n+-------PLWVVDGV--II--ED----VIE---L-G----A---------\n+------------D-------DL-----ASGDA--T-T----L------I-\n+---SS--AIAGL-NADDIEEFEVLKDGSATSIYGARA-MAGVIVITTKRG\n+-K--------AG--------V---S--TFNYSNETT--YRF-IPT-----\n+--------YDNFN----IM-N-S-Q--EQM--E--VYE-E-------FR-\n+----NA---------------GWLN---HS----D-----LVGR------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------SS-----------\n+-SGV------------------------Y-------G-------------\n+-------------------------KM-Y-E--L---------------L\n+SK---------------------V-D------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------A-------\n+--------------NG----N---------FLLANTPE-AKSAY------\n+---L-----RQAEL------------------------------------\n+--------------R--NT--N--WFKEL----F-S-----N--N-VMQN\n+HSV-SMSSG----N---DI---ATYYGSLSALVDPGWT-------L----\n+-----------------------Q---S-N--VNRYTANFNSSFK-L---\n+-----'..b'--------E-----------------T-\n+------LT-----------------------L------------------\n+--LT--N---LL-G----K-W------------------PNI--Q--AG-\n+-P------T--T--------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------PD-------\n+-GEV----------------------------------------------\n+----L---------L-----------------------------G-----\n+-------------------------------GSS---------YQ-----\n+------Y--S-------P---W----------------------------\n+-----------------A----Q---------I--------N--------\n+--------------R-S--G-Y--RK---ET-RS----------------\n+-SV-----N----ATFGM--SYD--LGF---------------LL-----\n+--K---------G--LSTKLTASY-------D---------T-Q------\n+----------S--------INYLVG-K-------KGY--Q----------\n+-------YWE-----------------------S----------------\n+---V---------VDP--NRK----N---------P--------------\n+----------------------------------------------DGS-\n+DYIE-----YHR--------IRT-D---YDNTP-L-S------T------\n+-S----------------K--SAT----------------FAS---FYDL\n+QWQINFN-RTF-----N-E---K-----H--TVTALLLAQKQSQ----IK\n+----------A-S-------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------DVL-----------------\n+--------------------------------------------------\n+-----P--FN---VQGLATRLTYA-YDD-KYIAEFNAGYNGSEQF--AP-\n+----------K-N--RYGFFPSASAAWNISREKFF--E------K-W--T\n+------N---V-V-D---KMKLRVSYGLVGN---DK-I------------\n+--G--NT-----------------------------R-FL----------\n+--------------------------------------------------\n+YL------DN----VA---------------R--------SY--------\n+----------------------------------------G---------\n+---------------G-----------Y-------------S-P--S---\n+-----L--S----------------------------------------N\n+NN-------------T-----------------------IQ-E-------\n+-L--F---FGNPNL-KWETAKKLNVGFELGLW-KY---FNLSFDIFSERR\n+DNILI-T-K--N-S---T---P--S------I---I---GV---------\n+------------------------------------ARST----------\n+--I--A-----PFNL--G-R-VKNRGYELEMSF-N-K-T-I----T----\n+--K--D--------LLIMAKANLNYND-NEVV--YMDE------------\n+----------L---K-----------F--D--------------------\n+--------------------------------------------------\n+E---------T---Y--A-Y--------PYHQTGYSIG-------Q----\n+---------Q-W---GMI------------------------AEG--FFK\n+--D-Q----D-----------EI------------------N--------\n+----------A-----Y---------------------------------\n+--------------------------------------------------\n+------------------------------------------------A-\n+--------------------------------KYEGQQ------------\n+P-R-----------------P--GDL------------------------\n+------KYK---D-----V----------------------------N--\n+---G--------------------------------------------D-\n+----N-----------------------I---------IN----------\n+-----------------------------------------Q--------\n+-----------------------K--------------------------\n+------D--------L--S------------PI--G--Y--S-D-V-PKY\n+TAGLALSITY-K-----NFDISALFQGAFN-----VS--G------A-V-\n+G---A--------------P--G-PY-----------E------------\n+-------------------------------------------------W\n+Y-------D----F--R------E-F--H---K-------K--------A\n+----W--T--------------A-------------------------ER\n+--------A-----------------------------------------\n+A-AG--EE-------IL-------------F-P-----------------\n+------------------AL-----A-L--A----------QS-------\n+--------------------------------------------------\n+----P---------------------------------------S-----\n+---E-I---------Y-NS---------------TF--F-NMDRSYIRLK\n+NLEIGYTLP------KN-W-S----RA---------I--N-A-KVVRFYV\n+NGYNL-A-T-W----D------------------KM---KF---K-D-W-\n+------D------PE-VM---------------DN---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------S--------------T--YP--\n+LLKVWNIGLNVTF---\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,5852 @@\n+>309807.SRU_1450\n+--------------------------------------------------\n+-------------------M-----SRPPRILIVEDEFAVAMELEDHLGA\n+--LGYTVVDHVMTGAAAIDRAA--G-----AD----LDLVLMDVHLDGP-\n+MDG---VEAARTIREDHP-LPVVFVTAYSDDETL-QRATDTT-PFGYVVK\n+PFNEREIYAAVEVAL------QTHALQRRV----------------ERAR\n+DDLRQLLNGLRQGTALTD-------------------GTG-R--LR-FLS\n+DPAARLLDVASEAATGT-PWADLLPV-------------DD-----EAL-\n+EALQSR---MDGTTDADGPVTATLAHDDGPSYRVEIEVRDDPRDSERHIL\n+VFYDVTEVHELRRMLDDRSR----F-HDLVGKSAPMQDAYEQIRSVA-E-\n+VKTTVLIQGETGSGKELAARAIHDESPR-----------SEGSFVTVNCA\n+ALNPDLAGSRLFGHRAGAFTGATEDREGYFEAADGGTLFLDEIGDVPLDV\n+QRQLLRVLEEEAVTRLGETEARPVDVRIVAATHRSLDEEVAADRFRQDLL\n+YRIRIARVALPPLRERRSDLPLLVRTFLREIRARTGADVDRVGDEALRRL\n+LNYDWPGNVRELKNALEAALIRAS-G-D--V--------LRADDLPPE--\n+-IR-----------------------------------------------\n+---------------------------------------E-A------S-\n+ASASSAPEEAERIRAALEQ-TDGNRT---EAAELLGISRATLYRRLDEYN\n+IE--------\n+>309807.SRU_1226\n+-----------MSTSLRAGRRKMEESSRALDRKENALYIGHLFFGHS-QP\n+LRAETGTAVTVHHRCKDPRI-----VMSKRIFVVDDEPKIGNLFSNVLER\n+--DGYDVDA-FVNPNSLLEALD--EDS---GE----PDVVVTDMIMPQM-\n+-DG---VELMEHLDERDLDVPIIIMTAHSSVQTA-VEAMRQGA-FHYLEK\n+PVNLEEMRALLEKAI------ELYGAQQELKQI-----------------\n+----------------------------------------K-----TE--\n+----------------------------------K---------------\n+----QKQ---YP--------------------------------------\n+------------------------I-EGILGESDPVVEVRETLETLCNA-\n+SNTTVLFTGETGTGKNLAAQTLHYNSPR-----------AEEAFTDIDCA\n+SLPDNLLEAELFGYEEGAFTDARDSKEGLIEVADGGTLFLDEIDSMSLAL\n+QAKLLSFLESREFRRLGGVEDKSADVRILCATNSDLEKSVQEDEFRKDLF\n+FRINVVNVKMPPLRSMGDDVLLIGRHIVSEFNREFGSDVSGFTNAAREKL\n+LNHTWPGNVRELRNVIERAMIFVE-G-D--Q--------IEAEDLTLAP-\n+-PS------RLDEREQ--P-------------------------------\n+----------------------------V--G--------N-NGFQFAL-\n+-GQTLKDVEKAYIRRTLETRADDSYAD---IADDLGISKKTLWDKRKRYD\n+LDEVVDR---\n+>518766.Rmar_0607\n+--------------------------------------------------\n+-------------------------MSKACVFVVDDEPKLGELFANVLRR\n+--DGYEVRA-FVHPQAMLEAI----ED--GQQ----PDVVLADLMMPEI-\n+-NG---IELLERLRKRRLHVPVIIMTAHSSVQTA-VEAMRRGA-FHYLQK\n+PVNLEEMRMLLKKAI------GRNERTSVSQPS-----------------\n+----------------------------------------P-----QG--\n+----------------------------------E---------------\n+----AAA---YP--------------------------------------\n+------------------------I-EGILGDSEPIRRVRQTIEMLRDV-\n+PGTIVLIRGETGTGKNLVARTIHANSCY-----------SSGRFVEINCA\n+ALPDNLLEAELFGYEKGAFTDARTSKPGLLEVADGGTVFLDEIDSMSLAL\n+QAKLLSFLESRTFRRLGGIDDIQVNVRILCATNVNLEQLVAERKFRQDLF\n+YRINVVNIYLPALREMGRDVLLIARYFIEQFNSELGRQVKGLTPEAEKKL\n+LDYHWPGNVRELRNVLERAMIFNR-K-E--W--------IDADDLHLLP-\n+-AT-----ASSNGVAL--P-------------------------------\n+----------------------------P--S--------N-GVFYFPS-\n+-GSTLEELEKAYILHTLK-HYKASFTE---AARMLGISKKTLWEKRKRYN\n+LDRELAR--S\n+>518766.Rmar_0508\n+--------------------------------------------------\n+------------------MSASPTRTSLDALVEIAQTINTLRDPEAVLEK\n+--VLEIAME-TLEAERGFILLK--A-PQHPEGFAIRSQRNFTDQQLGEL-\n+-VR---ISTSVVHEVLRRGEPVLVYEAQQDERYGKAESIVLQR-IQSIA-\n+-CVPLRIKERLIGAIYLDSLSQRGRFTRDNLPFLEAFAHQAAIAIEN---\n+------------------A------------QL-YQAL-RE-----EN--\n+----------------------------------RR-LR-----------\n+-SEIQRL---HG--------------------------------------\n+------------------------F-DEIVGQSPAMREVFDTMARVL-D-\n+TDATVLIEGESGTGKELIARAIHYNSER-----------KDKPFVVVFCG\n+SLPDELLESELFGYKKGAFTGALSDKKGLFEVADGGTVFLDEVGDLSPRM\n+QTALLRVLQEGEIRRVGDTQVRKVDVRVISATNKPLRELVQQGKFREDLY\n+YRLNTIQITVPPLRHRRGDIPLLAHHFLDKYAVKKRAHIKGFTPEALELL\n+ERYHWPGNVRELENTIERAVVLAR-G-E--L--------ITPEDLRLPD-\n+-TD---------------G-------------------------------\n+----------------------------A--------D-PF-E-----P-\n+-DLPLKEVERRVVLRTLKR-HGGNISE---TARVLGVSRRWLHYKLKEWD\n+VQNA------\n+>313594.PI23P_02332\n+--------------------------------------------------\n+-------------------------MNKLTVLVLDDEKRFTEELTEFLEN\n+--SGFQTFE-ANSAAQGLSLLK--K-----QS----IDLLILDVRLPGV-\n+-NG---LDILKKVKVKYPNMEVIIVSAHGDMDTV-IKAMRSGA-IDYLRK\n+PFRHIDIRIAIERTE------KFLFLQR----------------------\n+-----------------K-------------------V-K'..b'EIGNLSMPL\n+QSKLLTVLQRREVTRIGTNKAIPVDIRLICATNMHVHEMVMENTFRQDLL\n+YRINTVEIFLPPLRERQDDIPLLANHFLKSYSQKYRKNFEGFKPSAMELL\n+QRYNWPGNIRELQHAIERAIIMAE-G-D-------E---LDSRDFFFLS-\n+-AK--------------PA-------------------------------\n+--------------------SE------K--------AP--A------NN\n+-TLNLDDMERSTIQRAIDK-NGGNISK---AAKELGLTRASLYRRLEKYG\n+L---------\n+>880070.Cycma_3479\n+--------------------------------------------------\n+-----------------MEE-----KNLGKILIVDDNEDLLFAAKMLLKK\n+--HAKEVTI-EKDPRRIPFLIN--N-----NN----FDVVLLDMNFTEDT\n+TSGKEGFHWLKKIKEIDPKAVVILITAFGDVEMA-VQALKEGA-TDFILK\n+PWQNEKLLATLSAAI------KLKESYNQ---------------------\n+-------------------------------VDKLSSRQK----------\n+---------------------------------------Q----L-QA-D\n+-----LK-K--PF-------------------------------------\n+--------------------------SEIIGRSASMKNVFSIIEKVA-K-\n+TDANVLILGENGTGKELIARAIHDQSER-----------NDEIFVGVDMG\n+AITESLFESELFGHKKGAYTDAKEDRAGRFELADNGTLFLDEIGNLSMPL\n+QSKLLTALQKREVTRIGSNKSLPIDIRLICATNMPIHNMIMESTFRQDLL\n+YRINTVEIFLPPLRDRQDDIPILAEHFLKIYASKYRKEFKGLKHSAHQLL\n+QRYSWPGNIRELQHAIERAIIMAE-G-E-------E---LDSRDFFFLS-\n+-AK--------------PA-------------------------------\n+--------------------NE------K--------I---N------TN\n+-TLNLDEVEKNMIQKAIDK-NSGNISK---AAKELGLTRASLYRRLEKYG\n+L---------\n+>760192.Halhy_2462\n+------------------------MQ------------------------\n+----------------DKSD-----LHPGAILVVDDNSGVLTAAKLFLKR\n+--HFTQVET-ERNPENLPVLLA--N-----MR----YDVILLDMNFTKDR\n+SSGKEGFFWLERILQVDPSAVVILITAYGDVEMA-VQAIKGGA-TDFVLK\n+PWENEKLLATLFSAM------KLRASKVE---------------------\n+-------------------------------NDELKAKQK----------\n+---------------------------------------G----L-AI-A\n+-----HN-D--AI-------------------------------------\n+--------------------------PEILGNSTAMRKVFETINRVA-K-\n+TEANVLILGENGTGKELVAQAIHQQSNR-----------TNEHFVKVDLG\n+AITETLFESELFGHVKGAFTDARDDRPGRFEAANRGTIFLDEIGNLTAGL\n+QAKLLSALQNRMVTRVGSNQARPIDVRVISATNMPLYEMVKDRSFRQDLL\n+YRINTIEIHLPSLRERAEDILLLAEHFLQLYNRKYNRNISNISAALKKAL\n+LAYPWPGNVRELQHAMERAVIMAR-DSG-------T---LQPDDFMLGS-\n+-N------H-----S--LE-------------------------------\n+--------------------SE------A--------AL--N------AA\n+-TMNLEDMERETILKAIKK-HQGNISE---ASKELGLTRASLYRRLEKYG\n+I---------\n+>388413.ALPR1_08408\n+--------------------------------------------------\n+-----------------MSE-----YKSGKILIIDDNEDLLKAAKIFLKR\n+--HFAQVDT-ETNPDLLPILTH--N-----EN----YDVIMLDMNFTKDV\n+SSGQEGFYWLDRILELDPSAVVVLITAYGDVNLA-VRAIKEGA-TDFVLK\n+PWENERLLATLNSAL------KLRQKKLE---------------------\n+-------------------------------VDLLKDQKQ----------\n+---------------------------------------T----L-EQ-D\n+-----MD-R--KF-------------------------------------\n+--------------------------TEIIGQSPAMQKVYETIERVA-A-\n+TDANVLILGENGTGKELIARAIHRHSRR-----------SKEAFVGVDLG\n+SITQTLFESELFGHKKGSFTDAKDDRAGRFEQAHKGTLFLDEIGNLPLPL\n+QAKLLAVLQNRQVTRVGANRAVEVNIRLISATNMPIHNMVYDNTFRQDLL\n+YRINTIEINLPPLRERADDIILLANHFITFYSKKYNKDIRKASEPLLKRM\n+MKYHWPGNIRELQHSIERAVIMSN-H-N-------V---LQPEDLFLQK-\n+-MG-----Q-----P--EK-------------------------------\n+--------------------QE------E--------SV--S------LD\n+-HLNIEDVERILIRKALQK-HNGHITR---AAEELGLTRSSLYRRLEKYG\n+L---------\n+>643867.Ftrac_3412\n+--------------------------------------------------\n+-----------------MNE-----QKAGTLLIIDDNQDLLNAAKIFLKR\n+--HFKRVDI-ESNPNLIPTLLQ--N-----ES----YDIILLDMNFTRDV\n+STGQEGYHWLNKILEIDPSAVVVLITAYGDVNTA-VKVIKQGA-TDFVLK\n+PWDNEKLLATLHAAL------KLKNAGNK---------------------\n+-------------------------------VSQLESTQR----------\n+---------------------------------------Q----L-SA-D\n+-----ID-R--RF-------------------------------------\n+--------------------------RDIIGEGPAMQQVFETIKRVS-R-\n+TDANVLITGENGTGKELIARAIHRNSLR-----------DDKVFVTVDLG\n+AVTDSLFESELFGHKKGAFTDAKDDRAGRFEVAQNGTLFLDEIGNISLPQ\n+QAKLLTALQNRKITRVGSNKEIDIDIRLISATNMPIQDMIQSGKFRQDLL\n+YRINTIEIKLPALRERVEDIPLLTEHYIKFYSKKYNKEIYKVSDAAYSRM\n+CKYDWPGNVRELQHSIERAVILSN-Q-S-------V---LQPEDFFFQS-\n+-AD-----Q-----E--SK-------------------------------\n+--------------------RS------D--------KV--N------LD\n+-HLNIEDVEKILIRKALDK-NFGNITQ---AAQDLGLTRSSLYRRLEKYG\n+L---------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,2842 @@\n+>880070.Cycma_4201\n+-------------------MFQFID-P--K------F-RLLEA--LQVIR\n+---------KLFLPITF-SLTL-ICLTNGCGNKVAT--RD-----VPVDL\n+PEAY-S--L-----------PT-----G-------S---------SPMDS\n+NWWASFQDTLLNRLVDSAITHNLELKSSWFQVAQEAGNVAIIASQRVPQV\n+FLELQ-G-GASR-----PAPDF------------------------V---\n+-----GG-E---------NTQLSLRTSYEVDLWGRVKQSKLAAENRMIAT\n+FLDYQTMGISIAGEVALTWFTLQASREQMNLIKEQTEYNQQILALIRTRF\n+ASGQ-V--RGVDILRQEQLIENTKEEALALQMEIKILKNRLAVLLGKAPG\n+M-LNISE-KM---KLP--TLSPI-PNAGLPMELINRRPDIQSSFNQLEAA\n+DREVAVAISNTYPRLTFNF--TGALRS-N--TLTNLVES--Q---AASLT\n+GSLLMPLFYGGRLKAETHRAKAFREQQLNAYGQTVLLAVQEVEDALVRES\n+LQKEIIIKLENQLDLAERAFNQLRIEYL-NG--S--IAYLDVLVTLDQMQ\n+QLKRELVNEKLNLLLYRLSLYRALAGGFESPIENEEDFSIQENTISTK\n+>886377.Murru_2835\n+------------------------M-G--K-N----K-IEGYN--LNVKN\n+RQ--S-F-TV-LFLFSF-L--G-L-LYFNCSPRYSN--IS--PP---IDE\n+FQEFKS--S-----------GD-----------------------SLVSN\n+KWWEAFNDDKLNILIDSAMQSNLNLAATWQQFLSTRASVRSQASNKWPSI\n+EASAQ-T-ARTL-----PEPDF------------------------V---\n+-----GG-E---------NTQLGFLSSYELDLWGRIGTAVNAEKFRSEAS\n+YFDYQTLSLSLSAEIATTWYQLQAAKRQLQITEDQIKTNEAIIKLIRSRF\n+VGGQ-I--RAVDILRQAQLLENTKEQKIIFETNIQLLKNQLAVLLGKQPQ\n+E-GIVLE-EA---SMP--TVPKL-PKTGLPLELVRRRPDLKQSFATLLAA\n+DRDMATAVQSKYPRITLSG--RGQLRS-N--NFDNLFDN--W---AYSLA\n+GNILAPLFYGGQLKAEVDRATAVKKQRLYEYGQATLVAFREVEDALTQDM\n+KQAERLDNIARQLELAEKSNKQLRVEFL-NG--F--SPYLDVLLGLDQEQ\n+QLRRDYVAAQLQHVQIRITLYRALAGGFDTGRNLDDQKSKLDEFYEQ-\n+>313596.RB2501_06065\n+MPTIYCV----I-S-K--QFFSYGS-G--R-E----T-ATGVY--SAFSS\n+LF--SYV-FS-LFALLF-L--T-F-SFIGCGPSRES--IQ--PT-TGLDS\n+LQTLSA--A-----------GE-----------------------VPLPQ\n+RWWEQFDDPQLEGLIDSALTRNFNLAAAWERFRQAQFVLKREKGIRWPQF\n+EGGAQ-S-AISR-----PQPDF------------------------A---\n+-----GG-E---------NIQFGASAQYEIDLWGRIGTGLRAEAYRAQAS\n+LADYRTASLSLAAEVSLTWFRLKAARQQLALAKDQIQTNEDIFRLIRARF\n+GGGQ-V--RAVDILRQQQLLESTRNQRLIFEQNVALLEHQLAILLGKQPQ\n+A-IDPPE-AQ---DFP--ELPAL-PSTGLPLELVRRRPDIQQAYLTLHAA\n+DRDYATAVRAKYPRLSLRL--SGQQRA-N--DYESLFQE--W---AYTLA\n+GNIVAPLFYGGSLSAEANRSEAARQEAIYNYGQTVLTAFQEVEDALVQEQ\n+VQASRLEILEKQLDLAQKTNGQLRNEFL-NG--F--SPYLDVLLGLDQEQ\n+QLKRDLIDARLAQLEIRVGLYRALAGSFETEREIALNSEEKTTP----\n+>309807.SRU_0476\n+--------------------------------------------------\n+---------------------M-L-TVAGC-SMTPE--MS-TPE-AEQDL\n+PDRFEA--AP-----------GD--T-TLPAAAADT-------A-AYDAT\n+RWWAAYEDPSLTALVDTALAANLNLEEAQGRVEELAAQFRIARAPLFPSV\n+TANGQ-G-NYQN-----QPANTGIGGA-------------------I---\n+-----GG-GQGPDRFEFTDYQATLGLSYELDFWGRVRSQRTAALSQYFAT\n+AADLQTARLSVISQTISTYAQIASLRRQVRLGERTVGLLEERVAVTEDRY\n+ARGL-V--PSFQLYTVRQSLQAAQADQPDLERRLYEAQSRFATLLGRFAG\n+E--QRAL-LPDSMTVP--LAPEP-VPAGLPADLLMQRPDVRGAALRLEAA\n+RQEIGVARAEMLPSLSLTG--QGGTQS-S--ELADL-VDPGQ--VFASFA\n+GQLTAPLFQGGQLRANLNAAEARYKQQAARYEQTVLTAFQEVKASLVAYE\n+KQRQRYREVERQVDTARDAFQAQRDRYE-RG--V--GDVLSLIDAERTLL\n+QARTRLAGVRRAVTNARLALHRALGGPWTDAEPVDDPRLFR-------\n+>755732.Fluta_3866\n+-----------------------------------M--K-QHK-K--IN-\n+-PWIH-L-A------VL-----V--FLTSC-KVHQD--AL-KTD-I--SI\n+PQKFEA--E-A----PL---L--------------A-IDSVKKI-TETPE\n+KWQTFFKDPILVQLIDSALVNNLDMQIAFQKVQQARAGVQYTKGIRLPDL\n+GVNLGA--GVRR-F-GD---YTIDGVG------NYDTKFST----NLNNK\n+QQLPNPIP----------DFYVGVYSTWEIDIWGKLKAKKKAAFSRFLAE\n+EQGRNLVITNLISEIAIHYYNLMLLDRKRAIIAENILLQENALQVVGFQR\n+DIGK-S--NQLAIELISAQVLAAKTLLMEVDQEIIEEENTLNFLLGRYPQ\n+P-VFRS--EFNV--MP--ELTK-NELPGIPSDLLGNRPDILTAAYRLKAQ\n+NADVKAAKAAFYPNLTLNA--NLGYQAFR--AAFLF-ES--PASIAYNVV\n+GGLVTPLLNRRALKADLMASKASQQEAYLNYEKTILQAFTEVYQLVKLDN\n+NFESRSVVKNEQVALLKQSVETSRTLFS-S-G-R--AGYLEIITSQENYL\n+RSQIELLEIYRLKNQNNVHLYKALGGGWK-------------------\n+>649349.Lbys_2565\n+-----------------------------------M--K-----K---W-\n+-FKYI-V-I------GL--------VAGAC-KLPQT--QV-SVQ-E-KAL\n+PETFKG--S-A------------------------------DTS-HIGNL\n+SWRNYFSDPSLQALIDTALVNNLDKKMALERIQMAQAQVLAAKGAMLPTL\n+SGNFSP--ALRR-Y-GY---YTMDGVG------NATTDILP--------G\n+KRVPVDLP----------DFYIGLQSTWEIDAWKKLSNRKKSAYQQFLAS\n+VEGVNYVQTQLVAEVASAYFELVALDHELTVLSETVRNQEEVLDVIRAQK\n+EAAR-A--NELVVQQFKAQQLNTQTLERQVKQEISEVENRLNILLGRYPQ\n+P-IVRS--KDLL--FR--GLPK-DISAGIPVQVLHNRPDIKAAALEVESK\n+RLDVLSARAEFLPSIQLSA--G'..b'-S-------SAAVL\n+PWRSLFSDTTLQGLIQEGISNNLNLQTAILKISEADASLRASKAAYLPSL\n+DATIQ-A-TKAK-S-SQ---AALNFPAGTG--I------------NL---\n+-----NT-I---------TYQASLSASWEVNIWGQLSSLKRQALANYLES\n+DAAKRAVQTQLIADIANDYYNLLSLDEQLRVTEETVKNRIKDVETMKVLK\n+EGAI-V--NGAAVVQSEANRYSAEVSIPDLKQSIRETENALCILLARTPG\n+P-IKRN--KLAD---Q--VPSG-QLNAGLSTQLLRNRPDVQESEFAFRSA\n+FENTNVAHSYFYPTLTITA--SGGLSSLQ--LKNLF-DN----SIFYNLV\n+GGLTQPIFNKGQNKARYHIAQAQQKEAFNTFQQTILTAGQEVSNALYSYE\n+NAVSKQKLRAKQIQALEKSVSYTNELLR-YSS-S--TNYTDVLTSEQSLL\n+AAQLSGVNDRLQELQAIVNLYKALGGGWQQ------------------\n+>485917.Phep_1186\n+-----------M-N-T--R-----Y-HK-Y-Y------------------\n+----F-I-I---G--FS----I-L-TLTAC--VSRK--YE-RPA---VNS\n+NDLYRD--N-T---------T-G----D-------S-T-------TIASL\n+PWKNLFADAALQALIQQGINENLDLKQAIERIKIAEATLLQSKGALLPSL\n+TADLS-V-TDAK-Q-SR---AALNFPPGIN--I------------NT---\n+-----ET-Q---------TYKAQLSTSWEADIWGKLSSAKRSAYASLLQS\n+DAAKRAVQTQLIANIANGYYNLLALDKQLAITEQTIRIRQTDVETMKSLK\n+EGAV-V--NGAAVVQSEANLYAAQVTLPDLKRNIRETENALSILLGKGPG\n+K-IERG--TIDQ---Q--TVYS-NLQTGVSAQLLQNRPDVQAAEFAFRAA\n+FENKNVARSYFYPALTLTA--NGGLSSLS--FKNFF-DN----SVFYNLI\n+GGITQPIFNKGQNKARLKTAEAQKQIAFYSFQQTLLTSGQEVSNALYAYQ\n+TAAEKETTRAMQVASLTKAVDYTKELLR-YSS-A--TNYTDVLTSEQSLL\n+AAQLSGINDRLQKLQSVVNLYRALGGGWKE------------------\n+>485918.Cpin_4800\n+-----------M-K------------RR-Y-L------------------\n+----L-L--------LP-C--V-T-VVAAC-KVTKT--YQ-PPA---TDT\n+VAQYRG--Q-S---------L-S----D-------T-M-------NIARL\n+PWRSYFQDEDLQALIAEGLGKNLQLKAAITRIEAANVAYQQSKAAFLPQA\n+GFNAG-Y-KQSR----------LAYPQGFG--F------------VT---\n+-----TT-P---------QYDMSLSASWEADIWGRLRSAKKAAYISLLSG\n+EAARDVILTRLIADIAGHYYTLLVLDHQLTILEKAADIRSADVEAMTELQ\n+RSNV-V--NGAAVVQSQANEYAARVAIPVLKKQIRQTENALSILLGKPAG\n+D-IKRG--RLED---Q--LMPV-MINSGVPAQLLANRPDVRQAELAFRGA\n+FESTNIARTAFYPSLTLTA--AGGFSSFS--FGDWL-TK--NTGLFGNVA\n+AGVFQPIYNRGQNKSRLKVAKAEQQTAFYNFQQSLLTAGQEVSDALFTYS\n+SVEERKAFRSKQIEALEKSVDFTQTLLK-YSS-N--TNYIDVLTSEQSLL\n+SAQLEQANDQLEQWMAVISLYHALGGGWQ-------------------\n+>743722.Sph21_2599\n+-----------M-K------------YR-N-K------------------\n+----G-L-----I--VV-I--L-S-IVASC-KVTQK--YD-APD---AKI\n+ISNYRS--Q-T---------Q-A----D-------S-N-------TVASK\n+NWSDFFTDTALRKIIADGLEENLDLKMGIQRIVAAEAAFSQSRQAFFPEI\n+NGTAS-I-KRSR----------LAFPQGYG--L------------IN---\n+-----NA-T---------QYDAGLTMAWEADIWGRLKSSKKAALANLLAT\n+EAAQRAIRSKLVADIATNYYALLALDQKLKVLELTLENRKKDVLTMRELK\n+ASAV-V--NGAAVVQSEANQYAVEVLIPDIKRQIRETENVLCLLLGRPSG\n+A-IERT--ALSN---Q--KLPL-DLSAGIPVQLLRFRPDVAEAELVFRTA\n+FEQVNVAKTAFYPGFNITA--AGGFTSFD--ISEWF-TN--AG-LFANIM\n+GGLTQPVFNRGVNKARLKTAEAQQQEAFYNFNKTLLTAGKEVSDALFSLE\n+SASLKETSRRNELRSLEKAVDFTKELLR-YSS-A--TNYTDVLLSEQNLL\n+NAQMDRIDDQLQQWQAVIALYRAVGGGSQDYDDTERFVNN----QKNH\n+>471854.Dfer_5535\n+-----------M-K------------NK-F-I------------------\n+----G-A--------VV-L--T-I-LAASC-QVTKP--YQ-RPE---LTT\n+QGLYRG--E-S---------S-Q----D-------T-I-------SVASI\n+SWKQFFPDTALTQLITRGLEQNPDLRIAMQHIVAAKASLQLSKSAFLPDL\n+NGTLS-V-KQSK----------LAFPQGFG--I------------IS---\n+-----ST-T---------QYDLGLGSSWEADIWGKLRSAKRGALAGLLRT\n+EEARKAIRTELIADIAGNYYTLLVLDQQLAILEKTKKNRFADVKAVTMLK\n+EANI-L--NGAAISQSEANAYAAEIAIPALKNQIRETENALNLLLGQPSG\n+A-VTRT--TLDQ---Q--KANI-PLKTGVPSQLLQNRPDVKQAEYALWEA\n+FENTNVAKTFFYPALTITA--NGGFTSFN--FQDWL-TS--LG-LFGNVA\n+AGLTQPIFNRGANKARLATAKARQEQAAIELQKSMLIAGREVSDALYAYE\n+TAGEQREIRVKQLASLAKAVDANRKLLR-FSS-T--TNYTDVLTSEQNLL\n+AAELDAVNDRHRQWLAVIRLYHALGGGTR-------------------\n+>485917.Phep_1249\n+-----------M-K-------------P-Y-I------------------\n+----G-L--------LL-L--L-I-TLASC-RISKP--YQ-QPE---FDT\n+GKLYRD--A-E---------G-R----D-------T-T-------NIVSV\n+HWNKFFGDTILTGLIAEGLSRNIDMKIALQRIDAARANFQQSKAAFLPDL\n+NGNAS-I-KQSK----------LAFPQGFG--L------------IN---\n+-----SS-T---------QYDIGLSASWEADIWGKLKSTKRSALAGLLQT\n+EEARKAVQTQLIADIANRYFTLLALDQQLQVLEQTVNNRKTDVRTMKALK\n+AANI-V--NGAAEVQSEASQYAAEVAVPRLKKQIRETENALNILLARPPS\n+A-IYRS--SLDE---Q--QLLI-DLKAGIPAQLLQNRPDIKQAEYAFMAA\n+FENTNAARKLFYPSFNLTA--AGGFTSFS--LKDWL-T---PDGLFGNIA\n+AGLAQPIFNKGLNKARLITARTVQQEAALNFQQFLLKAGEEVSNALFAYQ\n+TAKTQQEIRVKQLAALQKSVDFTKKLLR-YSS-A--TNYTDVLTSEQNLL\n+SAQMEDIDDKLQQWQAVIALYRSLGGGSEN------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,4266 @@\n+>694427.Palpr_0330\n+---------------------------------------MNYN---LN-I\n+K-KGFL---PNEKVSTATTLKRLMSLIGIERKNLYIAMAFIFLNSGLSLI\n+GPYLMGHAVDSFVVTK----------------------------------\n+-----------------------------------QY-DGLI-KYSIILF\n+CVFCAALVSGYTQAQLMGRVGQRMLYNLRNTIFGKLQELPIDFFNQNKAG\n+DLISRVNNDTDKINQFFSQSLVQFMSSIFTMLGAGIFLLS-INVELGLAA\n+LAPAIALLVITRSISPWVKNRNAKNMKSTGSLSSEIQESLNNFKVIVAFN\n+RRDYFRKRFDEVNKENYQTAVKAGIANNIFTPVYGFSSNVGQMV-VLAFG\n+-IYLIA------H---G-Q------------------------F-SVGLL\n+ISFLAYINQFYNPLRQIAALWANFQVALAGWDRISQILQM-ENNLTV-Q-\n+--E-S-D-VK-EESCCLLSFRDVSFSYI--P-------------------\n+G-------NDILKNVSFDLERGKTYAFVGPTGGGKTTTASLMARLYDPTA\n+GQIILNGADIRSLDASTRTAKIGFILQEPFLFTGTLRDNILYGNQ-CFIG\n+LSNDELMDELKEVGLEGLLERFDGGLDAEIKSSGDGISLGQKQLIAFIRA\n+VLRRPDLLILDEATANIDTVTEQLLDEILKKLPK---TTTRIIIAHRLNT\n+--IESADEIFFINAGAVTKAGSMEEAVNL-L-------MKDKRES-----\n+----------------------\n+>487796.Flav2ADRAFT_0733\n+--------------------------------------------------\n+-----------MSKKKVSFRWAFKEFIWPRRKIVSLGLFLILVRSLSGLV\n+LPYASKNLIDEVIPSKD---------------------------------\n+------------------------------------I-EALT-YLLIVVC\n+IALLFQSVSSFSLTRLLSVEAQHLISILRASVQQKLLKLPISFFDNNKSG\n+ALVSRVMTDVEGVRNLVGTGLVQLFGGSITAIISLVILIK-INGQMTLFV\n+LVPVLIFAVIALKAFGYIRPIFRARGKINAEVTGRLTETLNGIRVIKGFN\n+AEDQEKDVFEKGVEELYQNVKKSLTATALMTSSSTFLLGLASAG-IMGMG\n+-GYFIM--N-------N------T-------------------M-TYGEF\n+VSFTLFLGFMIAPIVQMSNIGSQLTEAFAGLDRTQELMRI-PEENNL-EI\n+----R-T-LKLNQIEGNVSFKNISFSYD--D-------------------\n+K-------TDVLHDISFEAPKGSVTALVGSSGSGKSTIAGLATAFLNPNS\n+GKVLIDGVDLAKVDLKSFRSQLGVVLQDDFLYEGTIRENILFPRP-NA--\n+-TEEELLVAVEGAYVNEFTDRFEEGLDTLIGERGVKLSGGQRQRISIARA\n+LLAKPKIVILDEATSNLDTQSEAFIQKSLAVLMR---DRTTFVIAHRLST\n+--IQKADQILVVEEGDIVERGKHEELIKR-KGRYFELYTYQTRM------\n+----------------------\n+>880070.Cycma_4748\n+--------------------------------------------------\n+---------MAKNKSNVSLNSVFKTIIWPRRKYIFIGLVLIIISRLSGLV\n+LPWASKYLVDDVIPSSN---------------------------------\n+------------------------------------F-ELLK-WLIVAVV\n+IAVTVQAVTSFGLTQILSVEAQNLIAKLRVEVQAHIIRLPIRFFDNAKTG\n+ELVSRVMTDVEGVRNLVGTGLAQMVGGLLTSLISLVLLIY-ISPKMTLYV\n+LVPVIIFGVISLKAFGKIRPIFRERGKINADVTGRLTETLGGIRVIKGFN\n+AEDQETKIFESGVKKLFLNVKSSLTATSFVTSAATFLLGLASAG-IMGIG\n+-GYMIM--E-------D------Q-------------------L-TFGDF\n+LAFTLLLGFMIAPILQMSNIGSQLTEAFAGLDRTQELMNI-PLEADP-AN\n+----R-N-ILLPEIKGRVSFDNVHFEYE--P-------------------\n+G-------AEIIKGVDFVAEPGSVTALVGSSGSGKTTISGLVASFLIPTE\n+GTVSIDGQDLSKVDLNSFRKHLGVVLQDDFLFEGTIRENIMFPRP-NA--\n+-TEEMLQEAVKSAYVNQFTDQFEEGLETVIGERGVKLSGGQRQRLAIARA\n+ILADPRILILDEATSNLDAESEHFIQSSLKSLMA---GRTTFVIAHRLST\n+--IRQADQILVIEKGQIVERGKHDELIQS-KGRYHDLYTFQARI------\n+----------------------\n+>643867.Ftrac_2492\n+--------------------------------------------------\n+----MA---QQEQSSKTTLAKAFKTIIWPRRKYILIGLVLIIISRAASLV\n+LPGSSKILVDEIVPNAD---------------------------------\n+------------------------------------M-EMLK-WLIFAVV\n+GALIIQSVTSFILTQILSVEAQNLIAQLRSKVQSHILKLPIRYFDNAKTG\n+ELVSRIMTDVEGVRNLVGTGLAQMVGGILTSIVCLAILIT-ISPMMTLYV\n+LVPVAIFGFISLKAFGRIRPIFRERGKINAEVTGRLTETLGGIRVIKGFN\n+AELQEIRVFAEGVDRLFKNIKSSLTATSLITSSATLLLGLASAG-IMGIG\n+-GWMIM--N-------D------Q-------------------L-TFGDF\n+LAFTLYLGFMIAPIVQMSNIGSQLTEAFAGLDRTEEIMNT-PVETDD-PN\n+----R-T-IELNEVKGHIEFQNVSFAYE--E-------------------\n+D-------KDVVKNISFEAKPGSVTAFVGTSGSGKSTISGLVSSFLNPDD\n+GKIMVDGHDLERITLESYRSKLGVVLQEDFLFEGTIRENILFPRP-DA--\n+-TEAELLNAVRSAYVNQFTDKFEHGLDTEIGERGVKLSGGQQQRIAIARA\n+ILADPKILILDEATSNLDTESEHYIQSSLKELMK---GKTTFVIAHRLST\n+--IRQADQILVIEDGEISERGKHDELIDR-KGRYFDLYTYQARI------\n+----------------------\n+>388413.ALPR1_14594\n+--------------------------------------------------\n+-----M---AQTAARKITIGQVFKTIIWPRRRHLFLGLFLIIISRLASLV\n+LPGASKYLVDDVIPSND---------------------------------\n+------------------------------------L-NMLK-WLIIAVV\n+AAIVVQSVTSYALTQILSVEAQNLIAKLRSQVQSHIIKLPIRFFDNTKTG\n+ELVSRIMTDVEGVRNLVGTGFAQMIGGIITAIISLFLLIS-ISPKMTLFV\n+LLPVVVFGLVSLKAFGKIRPIFRERGKINAQVTGRLTETLGGIRVIKGFN\n+AEQQEIVTFGKGVDELFQNVKSSLTATSFVTSAGTLLLGLASAG-IMGLG\n+-GYMIM--Q-------E------Q--------'..b'+AEKTEYRKFERINTVHRDANIRSIWYYSVYYPVADVIAAAATGL-VVWYG\n+-AREIMH----Y------N------------------------V-TFGTV\n+TAFIIFIGLFFRPIRMLADRFNTLQMGIVSTDRILKLLDS-HEFT-----\n+VNN-G-T-FAPETLRGEVSFKNVWFAYN---------------------D\n+E-------EYVLKDISFDVKEGETIAFVGATGAGKSSVINLLSRFYDINK\n+GDILIDGTEIHEYELGALRRNIGVVLQDVFLFSDTIHNNITLGNT-SI--\n+-SRARIIEAAQLVGAHEFIERLPGGYDYNVMERGATLSVGQRQLISFVRA\n+LVHDPKIIVLDEATSSVDTETEELIQNAIEKLMK---GRTAIVIAHRLST\n+--IQKANKIIVLDKGEIQEKGMHDELLE-RGGFYANLYRMQYKEVMG---\n+----------------------\n+>313606.M23134_01627\n+-----------------------------------------------M--\n+A---DKEKAESKKILDWKTFRRLFDFIGAYKKYFYLLIFLTVLTAVFGPS\n+RPLLIQFAVDNYIVTG----------------------------------\n+-----------------------------------DY-PGLV-NISILMV\n+VILTFEAFLMYAHTYLSNWLGQTVIKDIRVQLYQHILRLRLKFYDNTPIG\n+RLVTRNVSDIETLSNVFSQGIASLLADVLLIFAILGVMFY-THWQLTLVS\n+LSLLPLLLLSTYIFKEKIKVAFDQVRAAVSNLNSFVQEHITGMSVVQIFG\n+SEANESKKFKEINREHRKAHLKSVLYYSIYFPVAEIISAGGTGL-LVWYG\n+-ARGVLH----E------E------------------------V-SLGVL\n+IAFIMYINLFFRPIRMLADRFNTLQMGIVSMHRILTLLDD-KDHI-----\n+PNE-G-D-YAPEHIKGDISFDKVWFAYK---------------------D\n+E-------DYVLKNISFEVKEGETVALVGATGAGKSSIINLLSRFYEINK\n+GTILLDGHDVNDYDLAHLRTKIGVVLQDVFLFSNSIKENIVLGNT-HI--\n+-TRDQLLTSAELVGARRFIEKLPEGFEYNVMERGSTLSVGQRQLISFVRA\n+MVYDPKIIVLDEATSSVDTETEELIQSAIEKLMK---GRTSIVIAHRLST\n+--IQKADKIIVLDKGEIKEQGTHTELLA-KNGWYAQLHKMQYKEVAE---\n+----------------------\n+>643867.Ftrac_2126\n+--------------------------------------------------\n+M---KKDDIKSGNIIDTSVLRRLYKFVKPYQGRFYFLVFLTLALAVLAPA\n+RPFVIQKAIDNPIAQG----------------------------------\n+-----------------------------------DF-QGLI-NMTLILV\n+GLLVMQAIVQYGHTYLSGWLGQYIIRDIRIKLYRHLLNLRLKFFDKTPIG\n+RLVTRNVSDVETLSDVFSQGLAAMIGDILQILFILGMMFA-MSWKLTLVS\n+LATLPLLFLSTYIFKEKVKVAFNQVRNAVSNLNSFVQEHVTGMSIVQIFT\n+AEKREYEEFKKINMEHKKANIRSVLYYSIYFPVAEVIQATGIGL-LVWYG\n+-AKGVVNEV-ET------G------------------------I-TLGML\n+IAFILYIQMFFRPIRLIADRFNTLQMGIVSSSRILNLLDN-KENI-----\n+PNS-G-D-YAPEKVKGDISFKNVEFAYN---------------------E\n+E-------DVVLKNISFDVKEGQSVALVGATGAGKSSIINLLSRFYDIQK\n+GEITLDGKDLKDYDLYALRQNIGVVLQDVFLFSDTILYNITLGNP-DI--\n+-SLKEVKAAAELVGARKFIERLPGGYDYNVMERGATLSVGQRQLISFVRA\n+MVYNPKIIVLDEATSSVDTETEEMIQNAIEKMMK---GRTSIVIAHRLST\n+--IQEADKIIVLDKGEIKETGTHQELLE-KGGFYHQLHNMQYKEMS----\n+----------------------\n+>880070.Cycma_0789\n+----------------------------------------------MG--\n+L---EKENIKSGDIIDTKVLRRLYTFVTPYKGRFYLLVGLTLLLALLAPT\n+RPLLIQKAIDDYVTVG----------------------------------\n+-----------------------------------DG-AGLL-RMTYLLI\n+GLLLIHAVVQFGHTYLSGWIGQVIIRDIRVKLYKHLLKMRLKYFDNTPIG\n+RLVTRNISDVESLSDVFSQGLAEIIGDLLQLIAILGVMFY-VDWQLTLVS\n+LCTLPLLIISTYIFKEKVKVSFNDVRNAVSNLNSFLQEHITGMNIIQVFN\n+RQEREYEKFQTINKEHRKAHLKSVMYYSIYYPVSEIIQAMGIGL-VVWYG\n+-ATGVFD----L------E------------------------I-KVGVL\n+ISFIMYLQLFFRPIRMIADRFNTLQMGVVSSSRIFNILEN-DEQI-----\n+PDE-G-N-NCPEKVKGDIAFNNVWFAYN---------------------D\n+E-------DWVLKDISFKANHGETIALVGATGAGKSSVINLISRFYDVNK\n+GAILVDGRPIKEFDLATLRKHVGVVLQDVFLFSDTIFQNITLGNP-DI--\n+-TKEQVLYAADLVGARRFIERLPGGLEYDVKERGGTLSVGQRQLISFVRA\n+MVYDPEIIILDEATSSVDTETEELIQAAIEKMMH---GRTSIIIAHRLST\n+--IQKADKIIVLNKGEIVEHGTHEVLLK-KDGFYSQLYQMQLKSVVVE--\n+----------------------\n+>388413.ALPR1_05090\n+----------------------------------------------MS--\n+L---EKEKHSSGEIVDTQVLKQLYRHVKPYRLQFYFLIFLTVALAALAPT\n+RPYFIQVAIDDYVAKG----------------------------------\n+-----------------------------------DG-VGLL-QIIYILV\n+GLLILQALVQWAHTFYSGWIGQVIIRDIRINLYKHLLKLRLKFFDNTPIG\n+RLVTRNVSDIETLANVFSEGLAAIIGDLLQLVTILAVMFY-IDWKLTLVS\n+LCTLPLMIISTYIFKEKIKVTFNDVRNAVSNLNSFLQEHITGMNIVQVFN\n+REEREFSRFKEINREHRAAHIKSVLYYSIYFPVAEIIQAIGIGL-VVWYG\n+-AVGVLG----M------E------------------------L-QVGVL\n+ISFIMYLQLFFRPIRMIADRFNTLQMGVVSSSRIFKLLDN-QEHI-----\n+DNE-G-D-LRPDSVKGNIKLEHVWFAYN---------------------D\n+E-------EYVLKDINFEVKSGQTVALVGATGAGKSSIINLISRFYEINK\n+GSITVDGNDIKDFELGILRKHIGVVLQDVFLFSDTIFYNITLGNP-DI--\n+-TEEQVWYAADQVGARKFIERLPGGLQYNVMERGATLSVGQRQLISFVRA\n+MVYNPEIIILDEATSSVDTETEELIQQSIDNMMK---GRTSIVIAHRLST\n+--IQKADKIIVLHKGEIVETGTHDSLLE-QGGFYTQLHQMQLKTMAI---\n+----------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,7665 @@\n+>709991.Odosp_1330\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MSCHGLKMAYRNLLKYKLQSVICVLGLAGGLSCFTVCNYMLRKELA\n+WNKQLPHYGETYKLVTIREN-----G--EV-D--E-------------LV\n+--SL-DLAEQLKQEF-P-EIEKSVY-YV-------G----MSG---V---\n+SD--K-LCV------V-----G------Q--ENGKQTAAKAFFVLTDSSF\n+FDFYD-FRLTAGNGEKLKKQPDVLILTSEGADKIFG--TS-----E-AVG\n+KSFTEVND----FK---------NT-ER--SWTVAAMMENFPH-RTDFQ-\n+YGDGVVL-NS-D-V-LR-Q---A---------------------R-----\n+YR-------D-Y-V-FVYYRLREGT-----S-YELLNR-K-I-GVYMEK-\n+----------HPE--W---R------------------------------\n+---------GNT-P-LTVKVYPYKDYKKLTGKP--------L---LS---\n+K-A-G------LIFSGIGLLVLLTALFNF-LLFTAGRMFNRRKELGIREL\n+HGATSGRLLQLFMVEITLTLLITGVIAAAMLELISM--YFAG----EWT-\n+-YYMNF-SEG------GS--WVIKMGGDLAEY--LIGV-WLLMLVVGYGI\n+IRQVR-Q----AT-----MLRNLQGG-----GIAYRARMQTVLLGIQLVI\n+CMFLIGLSWFMQNQQKALESQMAGGMTRAEMERIYAFNL-------N-GE\n+-----S---------LE--P--I--RKQMRDMLAANPYAEEWCRSG-TGL\n+L-A--P--W-M--M-Y-P---K-G----YRIE-G-V-EE--E-K-EVT-L\n+NYNCVDPNYTDFIHAKMEEG-RFF------K--T--------------G-\n+----------------EP--Y---V---MVVNRAFAD-WL-----GENPI\n+G-KSVTID---------------G---------------------M-M-G\n+V----------ITY----RIIGIMENLL-PVGNEPRI---IPGIYL-PFP\n+------E-G------Y--I---NET---LYVKFRP-G-----Y-VQQGIQ\n+PLKDKVQAQLSS-F-T---PLYIENLWVDMEGYLSKVIELGSMIFWLAVF\n+CILISALGVYSAMMLAVEKRSREMAIRKINGATLTDIAGIFCLHYLKLLI\n+FAACIAFPLIYGTMHR-WLEEYSHRITL--RPDVFAAIFILMMIIMLLTI\n+GSQLLKIIRVNPTEVLKND-\n+>203275.BFO_0866\n+--------------------------------------------------\n+----------------MQTKFFIDMNMN----------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+L----LRQYLKTGFRVFLKYKIQLSIAILGLAFSLVCFIPTVYWLHYETT\n+YDRFYSDAKEIYRIYAVEKG--S--G--KV-N------E---------Q-\n+V-PG-LLGNELLKYF-P-ILEATAG-FV------T-----EQ----L---\n+DY------Q------------T--------EE---NDYIQLKTLCVDSAF\n+LNVFQ-QPCVYGDMKQALQMAGNIVLTETVASRLF-GTAE-----K-AIG\n+QKLEHS-L-----SR---------I-FG--PCTVTAVVQDSPA-NTNLP-\n+F-DAIFN--F-P-A-LQ-D-A-S-M---------IM----S--T---SEQ\n+W-Q------Y-Y-NNNLYVKFYPQA-----N-SKGFEQ-Q-L-RNFTSR-\n+----------TN--K-----------------------------------\n+----------NT-D-IELRMLPISDVRHKLNS--------------D---\n+-QL-FTLN-FIRLLVISSILLMLSALFNF-LNLYLGLFRQRINEFRQRMI\n+HGATSRQIITQMMFELTCVVLSALLIGTFFIFLTRP--VASNLLGIVMP-\n+-TP-QL-IYF-------S--LLSGLGIMLFVL--LFSL-IPCWRMNQLIT\n+RNMAE-------R-------KASN-------QPML----QRIAISFQLAV\n+SIVFIIAASVTMMQMRFINQKDL-GFDR---GGIIQLYSE--------NM\n+------------K--LD--E--H--KATIKQRLEAIPQIMNISATD-YSP\n+D-KN----A-T--VTT---E-V------E-WP-G-K-QLH---K-KPV-F\n+QWLFADANFAKTFRLKLIA-GRWWEEGQ--NEN-----------------\n+------------------HK--------VVLNEEAVK-VMG--LS-----\n+----------EPI-G-SII--------RMNPFL-ITND-GV----A---P\n+M----------EEY----EVIGVVNDFH-SHSLRSR--IH-PTIIR----\n+--TGLE-----N--I-------------WYIRVVP-G-----Q-EQEVMQ\n+RISSILT-DIDIRL--T--DTRLTLLDEVYDRLDYSEQIGLKLFFILAIV\n+CLSISLFGIYAIARSTTQKRRKEIAIRKIFGADIQNVVRMFVCEYSLLVV\n+FAAAVALPIAHYVMYR-WLHGYAYHTNI--PWWLPVMVFTGSITLVLFTV\n+LGQVLKAAGSNPAKVIKSE-\n+>435591.BDI_2836\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+M----LIHYCVIAFKNIWKYKVSASISILGL'..b'-SS-S--RSD---T--T---FS--TE-T-V-MTE-S-N-GFN-M\n+QYWNIDYDYIETIGMEMKT-GRNF--S---R--DF------G--------\n+--------------SD-S--T---G---IILNETAVK-LAG--F------\n+---I------NPI-G-KKL-Y--T--------V----D-SD----NST-Q\n+------------AF----TIVGVVKNFN-FASLREN--VG-ALCFQ-L--\n+G-N--------N----------SWE---TAFRFNA-K-----D-VSGLLS\n+TIENKYKA-AAPG---M--PFKYEFLDEAFDNMYRQERRVGKVALAFALL\n+AIIIACLGLFGLATYIAEQRTKEIGIRKVLGASVSNIVRMLSTDFVKLVM\n+LAFIIATPIAWWFMGK-WLEDFAFRIEL--NWWVFAVTGIVALLIALITL\n+SFQAIRAAIANPVESLKTE-\n+>761193.Runsl_1946\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+M----LTNYFKIAWRNLLKNKIFSFINVAGLAIGLCCFIMIALYVTDELS\n+YDRFHEKADRIYRVHADIRF--G--G--TD-L--K--LA---------V-\n+S-PD-PMGATLKKDY--PQVEQYVR-LY------T-----SD----G---\n+AK-----SI------K-----K------G--K---EYIVENHVGYADSTL\n+FEVFT-LPALAGDTKTALDNPNTVVVSESAARKYF-G-TT-----D-AVG\n+KTLEV--G-----VT---------D-KT--LYKVTAVIKDIPA-NSHFN-\n+F-DFIFS--M-D-N-V--P-Y-E----------F--------------GN\n+Y-L------S-N-NFYTYILLREGT-----D-YKAFEK-K-F-DEVA---\n+---V--R---YI--LP---Q-A--K-QYM-QIN-SMDEFK-------K--\n+--------A-GN-Q-LEYHLMPLTDIHLKSDR--F--P------EIG---\n+I-N-GNIQ-YVYIFSAVALFLLLIAGINF-MNLSTARSSNRAKEVGIRKV\n+MGTERQTLIAQFMAESTLTSYLAFLFALLLTVILLP--YFNDISAKTFS-\n+-IS--S-LFQ--P---RL--LSFLLILPFAVG-ILAGY-YPAFFLSSFRP\n+IEVLK-S-----K-----L-NAGF-K-----RSNL----RNMLVTFQFVT\n+SLVLVIGTIIVYRQLNYIQTKKL-GFDK---DQVLIING-------T-G-\n+-----A----L----TA--N--R---DAFKNEVGQMAGVKSASYAG-YLP\n+V-A----NS-A--RSD---N--P---FS--KE-A-V-MDM-K-N-GFN-M\n+QVWNVDYDYVPTLGMEIIK-GRNF--S---K--SY------G--------\n+--------------SD-S--S---A---VIINETTAK-ILG--Y------\n+---D------DPI-G-KKI-Y--T--------S----T-GA----LAG-M\n+N---T-------AY----EIVGVVRNFH-YESLRQQ--VG-PLCMK-L--\n+G-N--------N----------SWT---AAFKINT-E-----E-VQSLVG\n+QIEAKWKA-MAPE---M--PFSYQFLDESFDQMYRTEQRVGKVALTFAIL\n+TILIACLGLFGLVTYMAEQRTKEIGIRKVLGASVPSIVGLLSGEFLVLVV\n+ISVLIASPIAYYAMSQ-WLTEFAYRIEI--SWWMFLTAGILAVCIALLTV\n+SFQAIRAALMNPVNSLKSE-\n+>760192.Halhy_4095\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+M----LRNYLKIAWRNLLKNKTFSSINIFGLAIGLSCFILITLYVVDELS\n+YERFYPNAARTYRVDSDIRF--G--G--TD-L--N--LA---------V-\n+C-SD-PFGATLKKDY--PEVEQYVR-FY------A-----SD----G---\n+RK-----FI------K-----R------G--T---ETIIENRVAHVDSTY\n+FDVFP-RPILAGNPKTALDEPNTVAISESAAQKYF-G-TT-----D-ATG\n+KTLEV--G-----IN---------E-KT--IYKVTAVYADMPS-NSHFH-\n+F-DFLFS--M-D-N-VT-D-Y-N----------Y--------------GN\n+F-L------S-H-NFHTYIRLREDA-----D-PRALEK-K-F-PDLI---\n+---N--R---YV--LP---Q-A--Q-GFM-EIK-SMADFE-------K--\n+--------S-GN-K-LSYSLIPTTDIHLKSDR--L--V------ELD---\n+V-N-GNMQ-YVSVFGIVALFLLLIACINF-MNLSTARSANRAKEVGIRKV\n+LGTERQTLIGQFMAESTLTSYLAFAFALGLVALALP--YFNELAAKTFS-\n+-IT--M-LFS--P---RY--LPFLLLFPLAVG-FLAGY-YPAFFLSSFRP\n+IEVLK-G-----K-----L-NTSA-A-----KSNF----RNALVTFQFAI\n+SLLLIISTVIVYKQLNYIQSKNL-GFDK---DQVLIINA-------T-S-\n+-----G----L----ED--N--K---EAFKNEIKQLTGVKGACYAG-YLP\n+V-D----NS-S--RSD---N--T---FS--KY-A-V-MDA-K-S-GFN-M\n+QIWNIDHDYIPTLGMEMAK-GRNF--S---R--SY------G--------\n+--------------AD-S--S---G---IIINETAAK-ILG--Y------\n+---P------DPI-G-KKL-Y--T--------S----D-GN----SST-Q\n+T---I-------AY----TIVGVVKNFN-YQSLREN--VG-PLAMR-L--\n+G-F--------N----------RWE---TAFKVNM-S-----E-APNLIA\n+QIESKWKQ-MAPA---M--PFKYQFLDEAFDEMYRAEQRIGKVALTFAFL\n+TILIACLGLFGLVTYMTEQRTKEIGIRKVLGASVAGITALLAKDFLKLVL\n+IAILIASPLAWYFMSK-WLANFAFRINI--QWWMFVGAGVLAVLIAFLTI\n+GWQSMRAALANPIKSLRSE-\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,9030 @@\n+>309807.SRU_2167\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------------M--\n+------HTRFD--SNS--GGTQG------DNP--I--RHRLDTEALAPIH\n+TRA-LF--RICRPPRFMPTHLSSTVRA-IVRP------N---A-------\n+--------------------------------I-PVT-GLLI--------\n+---------------GVVLLIGGRRPAQAS-RLASGA-RAA---------\n+--------------------------------------------------\n+-------ADTT-APIVHEVDIRGNRQF-A-SGTL--KENIR--T--RPNR\n+RV-----LGIPG-----LTWWRWV-HQLG-S---AD-WM--WER------\n+------LGRALR--------------------------------------\n+-------------------------------------SGGEP-PAYIDST\n+TVGGDAERLELFYRQRGFRDASVSYRVE-----P-R--E-E-DDRVRVVF\n+EIEPGSATHLRRV-TYAGL------------DALRTGQKQRLVDGTVFET\n+----A--S-V---------------------S----MGDT------L-SV\n+RVQG----QRYREPMLLEERRRILTFLQNEGYAAVSRDSVR--AV-----\n+----------V------------YRAT---------PD------------\n+-----------------------S----FDV---TLRV------------\n+----------QTGPRYRFGDVRF---------------------------\n+------------EATGPEDAPPRSD---------------T---------\n+----------VD---V---AVDTTGG-GR------PQVT-A----RF-VD\n+-------ERRLDPAIVRRSLRFTP-------------------GAYYDQS\n+AVQATKRRLDGTGVFAFTN-LSPQYE--D---A---VRR-----------\n+-------------DTTGAPYLPLQINAQTRQRHRLQAETFALQRESVGAR\n+E---AG----VRLNEFGVGLSGTYENVNAFGGGETFRLRTSASVATGLDS\n+---------------------------------LLVSS---N-QFEGSAS\n+LVLPYLIRP-FQSL-D-----R----------------------TF----\n+------------D--L-SSARTRLSLTGLTALR------TDLGLRIRSRV\n+NAQLRLEMD--H-TP-TQSSLVDVVDLSL-SNP----DTL--DQFS---K\n+K-F-LRRVFG-RGGDNL---------------------------------\n+-----------------------Q-D---------------PVQR-----\n+-------------------------Q---------QILED-YTQPQVNT-\n+-----AVRYTFRDATAG----P---------MRRRSGHIYEASGEVGNTL\n+PLLLDRFVFTPG--R--P-D-YSLPSLFGGAG-GLTG---QLIYRPYVRA\n+SVDLRRYVPL-GSG-----TTLGLKFFGGWAHPTAG-------PT-----\n+----VV--PFDRRFFSGGANSVRGWRLR-ELGPGEGL-P-----------\n+-------------------------------------ADTTTAVPESPSN\n+ILGGDVKLESSIELRTTL---FPS-------VLAARWIGATFLDVGNVWF\n+GP-RNRG--------------FG-QA--D------------DNR--DG--\n+--PGAA-RDG-RDGRFAGP--EALLDVGVGGGAGLRLEWP-YLIVRLDLA\n+YRLHDPS-PR------N-----D-D-V-----FG---DN-----------\n+-----------------------------FSG-PLLHFGIGHS--F\n+>518766.Rmar_2555\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------MLLCLIGW\n+GLLGGLPVWGQTQQQFFSE-------------------------------\n+--------------------------------------------------\n+----------------AWLVRDV------R-LEGNR--------------\n+--------------------------------------------------\n+-------------------------SF-S-DEIL--RPYIH--T--TANR\n+RF-----LGIPG-----LTWWLWL-YKLG-A--SGK-LG--G-L------\n+------LSRALM--------------------------------------\n+-------------------------------------ASGEP-PAYYEPA\n+VVQADVERLTLFYRQEGFPRARVEARLD-------T--L-R-PGQLRVIF\n+HIDEGPPTYLRHV-RYEGI------------ETLSPE-LQRALLAG-SRL\n+---RHDPPTD--------------------------T--S------R-QL\n+RARD----QRYSELMLLEERQRLMDFLWNAGYAAVTRDSIR--AI-----\n+----------V------------IPAR---------PD------------\n+-----------------------S----FDL---IFRI------------\n+----------HPGPRFRFGDLEA---------------------------\n+------------EVDGPE---PDPFF-RR---------D-TLW-------\n+-----LEP-AAD---T---LA---PG--R------LV---V----TR-RQ\n+-------ERRLKPSFLARMLRFRP-------------------GDWYNRA\n+LLLSTRRRLEATGLFSYVR-IEPAWR--D---T---LRL-----------\n+-------------PGEAAPRLPHRLTLTTRPRHRMRLETFMLQRNGLLTG\n+S---E--------NELGTGVAVTYENANLLGRAETFSLRTAGSISGNFEE\n+---------------------------------GLLTS---A-QLEITAS\n+LVYPYAVRP-FGA--L-----E----------------------RW----\n+------------L--RLYDARTRLSLSLLTARR------DVLRLVIRGRG\n+TARFRLELQ--H-TP-TLTSFVDLLDLSL-SNP----DTL--SGFR---A\n+T-F-LDEVLR-PI-------------------------------------\n+-----------------------E-D---------------PVQR-----\n+-------------------------A---------QILDD-YTVPQIND-\n+-----VVRYTLQSARFN----P---------LRRERGYAHELSVETGGLL\n+SDLLDRTVFTPG--R--H-E-GTLPGLPLFRSGATGN---RLLYRP'..b'-----------------------------------\n+------AAK-V-A------------KT-V-KAEL--EPILR--P--KPNK\n+VI-----LGF-----P---YKVWM-YYF-LG-EP-KK-EK---SFKGWF-\n+--------------------------------------------------\n+-----------------------------------RKKFGEP-PVFASKR\n+TVTTNSLVITGYLNNEGYFRSNAAGELM-----------EKK-RLAKAIY\n+TVGLRKRYTIKSV-EFVT---K---DT-SVFS--------KNLK------\n+--------LT---------------------Q-------K------NT-L\n+LKEG----QPYRLSVIEEERSRIERDLKKHGFYYFRPDYL--IVK-A-DT\n+N-------------------------L---------SN------------\n+--------------Y--------Q----TNL---SVEL-KP---------\n+------NTTQLALKTYFIQNIYVIS-------------------------\n+--------------DDGR-------L--K------KD-------------\n+--------------T-LAGI----TG---R--RG--S---IRVID----A\n+-------AQAYRPRIFYDAIGFRR-------------------GTLYNSE\n+LHDVSLSRLINLKNFKFVK-NQFELL----P-R---SD------------\n+-----------------SALLDVYYYLTPLKKKTLRAEISAV--------\n+---------TKSNNLTGSQIGLTWLNRNLFRSAEQLRLNANVGLDVQLG-\n+--G-RSI------N-----------K---N-VS---NF----YRTSFEAE\n+LSFPRFVLP-FY-R---------------------------VR-PER---\n+--------------N-QTLPKTTLTTGFERLTQ------QGLYTQTSVKL\n+NWGY--SWR--K-NT-EIEHSFLPIALNVVQP----SN--ISPALVDS--\n+----I---------------------------------------------\n+------------------------FS---------------TNAT-----\n+-------------------------LQ-DIQRYFRILENR-L-----ILG\n+A----QYNITYTP--TP----R---------PLSKNSFVMLGGIDIAGNI\n+AGL---FSKKGD-N--V----------------REVF--G-VPYEQYARF\n+DAEVRYYRNI-SPK----L-RWANRILTGVGIPYGN-S------L-----\n+----SL--PQFKQYFAGGTNGIRAFRAR-TLGPGS-YQQ-----------\n+----GPLT------------------------S--SI----------FGN\n+ASFGDIRLEANSELRWRISQY---------------FEGAMFADAGNIWM\n+YR-D-FD--------------DSFYPP-----------------------\n+-EDN--A-VFT-------N--EFYKQIAVGGGLGLRIVTP-FVLLRFDLA\n+VPFRKPWLPE-------------NE-----RW-VFNQFA-----------\n+------------------P--R--SKPWRKEN-LVLNIAVGYS--F\n+>471854.Dfer_3196\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------MRSNI-G---YLLAI--CIFLGS\n+CSVN-R-----YVPEGQSIYVGN------K-VNVQAD-TLS---------\n+--------------------------------------------------\n+------KPN-V--------------SG-L-SSQL--EGLIK--P--PPNK\n+TL-----FGF-----P---WKVWF-YYW-IG-EP-KD-EG---GLRSWF-\n+--------------------------------------------------\n+-----------------------------------RKKLGEP-PRYATQR\n+IVDINAANMVAYLDNEGYYRSSVKGKIV-----P-HK-KKKK-RTAVTEY\n+NAYVMPRYVINEL-TYVI---P---DS-SRFN--------RDLD------\n+--------SA---------------------K-------A------KT-L\n+LKKG----DPIRLDVVSAERTRIDQELKGKGYYFFNPDHL--IVK-V-DS\n+T------IGGA------------DSTL---------GP------------\n+--------------Q--------Q----VNL---YLEV-KK---------\n+------ETAQTSLKQYFINRIFVNT-------------------------\n+--------------GTEE-------S--Q------QT-------------\n+-----------DSTA-LATR----GP---L--RR--G---INVTD----P\n+-------GNKYKRRIFYDAIGFRR-------------------GNMYTNT\n+MHDVSLQRLVNLQNFRFVK-NRFDLV----P-R---SD------------\n+-----------------SALLDVYYDLAPMKKKSLQTVLSAS--------\n+---------TKSNNLGGSQLDVTWRNRNFFRGAEMLALSAYFGFDVQLG-\n+--G-NRN------SS----------N---N-IG---NE---YIRYGAKAD\n+LSFPRFIIP-FV-R---------------------------IR-PEK---\n+--------------S-QALPKTILSLNYENRIQ------RNFYTTRSIRG\n+DWSY--VWR--R-NS-EVEHTLTPISINFVEP----RN--INYETYDK--\n+-I--I---------------------------------------------\n+------------------------FD---------------PDTN-----\n+-------------------------PL-DVQRYLTILETKYL-----IMG\n+S----NYSISFRP--TP----R---------PFSKNQFALSGGIDYGGNL\n+LSL---IAKKME-Y--DS---I----------PRELF--G-VPVFQYIKL\n+DGDVRYYRTI-TPS----I-KWANRLLLGAIRPYGN-S------K-----\n+----TMQTPLFKQYFGGGSTGIRAFRAR-SLGPGV-YPP-----------\n+----DSSS------------------------I--AL----------FGY\n+QTFADIRMEFNSEIRIKFTDI---------------INTALFVDAGNIWS\n+FG-S-AE--------------RSGY-------------------------\n+-DER--A-LIS-------N--DFFKQLAVGGGIGLRLDFS-YLVFRLDLA\n+TPFRKPWYTQEIESETP-----EGDIKYKNPW-VFNEIK-----------\n+------------------F--G--SKSWRKEN-LILNIAVGLP--F\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,2373 @@\n+>309807.SRU_0301\n+MMPASGRPWVVCKFGGTSVSSRARWDTIVEVVRTHRAEGRAPFLVCSALQ\n+GISDQLEALCAQLASAEPGAPESTLNTIRERHRALGQDLGVEAEAVLSGE\n+FARLERWVDEIQATDGPSPRQRAAVLATGELLSTRLGAAYLSAQGLPAEW\n+LDAREFLRATDDPHLPPRRQYLAANCTSHADPGLQARLADAPETVYLTQG\n+FIASNALDETVLLGRGGSDTSAAHFAAKLEAERTEVWTDVPGLFTANPGE\n+VPSGRLLRRLDYDEAQELATMGARVLHPRCLDPARRHQIPLHVRSTEAPS\n+LDGTIVSGEGPDVGPQVKAISAKTDITAVSMDTLGMWQEVGFLADVFQVF\n+KHHGLSVDLMATSESNVTVTLDPVANALDPDILDRLLHDLNRYCDAELID\n+PCAIVSLVGRHIR-SLL--S-ELGPAFE-VFDEQKVHLVTQAASDLNMSF\n+VVDEDQASRLVRELHAQFFGHRAPDAVFGPRWQELVEDGTPEETPDVWWR\n+ERREALLRLADDESPRYVYDPEVVTARSDEVQGLGPID---QSFYAVKAN\n+PHPEVLRLLERRGLGFECVSPGELDRVFEACPGLDPARVLFQPNFAAPAE\n+YADAFERGVH-VTVDNVQPLAEHPDVFAGE-----ELFVRVDPGQG-EGH\n+HR-KVRTAGAQSKFGVVPDDLGRLRAAV-DQAGATVVGLHAHVGSGITDE\n+STWAGLVDLLASLAAEFPA----VRALNVGGGLGVPNASGGRPLDLDALD\n+AALGKAA------ARHPQYDLWMEPGRYLVAEAGVLLARVTQTKT-KDAA\n+AYVGLDTGMNSLLRPALYGAHHEIVNLSRLDE------------------\n+-------------------------PPAMTADVVGPVCETGDVLGHDRRL\n+PPTEPGDTLLVATTGAYGASMSNRYNLREPASEVM--------------L\n+APEPA----------------------------------------\n+>518766.Rmar_1656\n+--MASP-RWVVLKFGGTSVSTLPRWETIARIVRDRLAEGLRPVVVCSALS\n+GISNALDR---LLAEAMAGRGEAALEGIRRPHLELGRAMGLDAEALLRPY\n+FEELERITLGAALLREVTPRLQARVMAMGELMATTLGAAYLNRIGLTTQW\n+WDARELLEAVDEAHGNEARRYLSVACDYRPDPALQERLAAAPAEVILTQG\n+FIARNSRGETVLLGRGGSDTSAAYLAAKLQAERLEIWTDVPGMFTANPRQ\n+IPSARLLRHLDYDEAQELATTGAKVLHPRCLEPVRAYGIPLHVKCTDHPE\n+LEGTIVSADAPDVGPRVKAISCKTGITLVSMDTIGMWQQVGFLADVFGVF\n+KRHGLSIDLIATSETNVTVSLDPQANALQPAQLEALVEDLSAYCQARVIA\n+PCAVVSLVGRHIR-ALL--D-ELTPAFE-VFAEHHVYLISQAASDLNFSF\n+VVDEDQADRLVRRLHAELFGRVEADTLFGPTWRELFAPRAEAAVARPWWH\n+HRRSELLALAEAQAPCYVYDEGTLRGQLEALRRLSSVD---RIFYALKAN\n+DHPDVLRVFHEAGLGFECVSAGELEHVRTLFPELAPERLLFTPNFAPADE\n+YRRGFELGAF-VTLDNLHPLE-AWPELFRNR----NVLVRFDPGRG-DGH\n+HR-YVRTAGAQSKFGIAPAQAKRLRELA-DRLGLRIVGLHAHVGSGILLP\n+ETWAETALFLAELAETYFPD---VRYLDVGGGLGVPERTGAPGLDLEAVE\n+AHL-HRF----K-TAHPRFELWLEPGRFLVAEAGVLLARVTQVKE-KGGA\n+RYAGVETGMNSLIRPALYGAYHEIVNLTRLDA------------------\n+-------------------------PATQTVDVVGPICETGDVLGHGRRL\n+PDTREGDVLLIAQAGAYGAVMSSHYNRRPPAREVF--------------L\n+PVGASAAVSPTPENAASV---------------------------\n+>908612.HMPREF9720_2223\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M--L-SRQIAQK--L--RGY--------------\n+--------------------------------------------------\n+------------ETPFYLYDTALLRQTLESVVYESKKY-GYKVHYAIKAN\n+YDDHLLAIIREYGLGIDCASGNELRKAVE--AGFDPKGIVYAGIGKRDKE\n+LRYAIGQEIMAINCESIEELE-LVDRLAGEAGKKTDVALRINPDID-PKT\n+NH-CIDTGQADSKFGISYEEVLEHAKEIKSLKHINIVGIHLHIGSQIREL\n+HVFENMCNKVNVIVENLEKLGFSFRFVDVGGGLGVNYDVPEN-EPIPNFA\n+SLF-SIVHN-HL-AV-GDREVHFEFGRSIVAECGELITTVLFNKTTATGR\n+KLVIVDASMTELIRPALYGSYHNIENITS--E------------------\n+------------------------DEVREKYTIVGTACESTDVFDENVTL\n+RKTRRGDLLTLKSAGAYGMSMASRYNLHDLPGAVY--------------S\n+DEIR-----------------------------------------\n+>717959.AL1_05600\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M--L-SRQIASK--L--RGY--------------\n+--------------------------------------------------\n+------------ETPFYLYDMALLRQTLESVVYESKKY-GYKVHYAIKAN\n+YDDHLLAVIREYGLGIDCASGNELRKAVE--AGFDPKGIVYAGVGKRDKE\n+LKYAIEQNILAINCESIQELE-LVDALSAEAGKVTDIALRINPDID-PKT\n+NH-CIDTGQADSKFGISYEEVLEHAAEIRSLKNVNIIGLHLHIGSQIREL\n+HVFENMCNKVNVIVENLEKLGCKFRFVDVGGGLGVNYDVPEN-EPIPNFA\n+SLF-SIVHN-HL-'..b'----\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M--N-SKDLLQL--T--EQF--------------\n+--------------------------------------------------\n+------------GAPLYVYDADKITSQYKKLTNAFKGVPNLKLNYAAKAL\n+SNLSILRLLNSLGSGLDTVSIQEVKLGLL--AGFKPESIIFTPNGVSLEE\n+IEEAAALGIQ-VNIDN---LS-ILEQFGSKHP-DIPVCIRINPHVM-AGG\n+NS-KISVGHIDSKFGISIHQIPHLLRIV-ELTNMNINGIHMHTGSDILDI\n+DVFLYASEILFETAKNFKD----LEFIDFGSGFKVPYKEGDIQTNVDELG\n+KKLTTRFNE-FCKEYGKELTLAFEPGKFLVSEAGHFLAKVNVVKQ-TTST\n+VFASVDSGFNHLIRPMLYGSNHQIINISNP-K------------------\n+-------------------------GKERYYSVVGYICE-TDTFGSNRRI\n+NEISEGDILCFQNAGAYCFTMASNYNSRYRPAEVLWFQGKAHLIRKRETF\n+DDIL--------------HNQVDVKGLFESPKKQTV--------K\n+>313603.FB2170_00950\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M--R-NADLLKI--A--KTY--------------\n+--------------------------------------------------\n+------------GNPVYVYDSEKIISQFNRLTNAFKGVNQLKLNYAAKAL\n+SNIAILRLMNSLGSGLDTVSIQEVQLGLL--AGFKPESIIFTPNGVSLEE\n+IEEAAKLGVQ-INIDN---LS-VLEQFGGKHP-DIPVCIRINPHVM-AGG\n+NS-NISVGHIDSKFGISIHQIPHLLRIV-ELTKMNINGIHMHTGSDILDI\n+DVFLYASEILFETAKNFKN----LDFIDFGSGFKVPYKEGDIETNIEELG\n+KKLTGRFNE-FCKEYGKELTLAFEPGKFLVSEAGHFLAKVNVVKQ-TTST\n+VFASVDSGFNHLIRPMLYGASHTIENISNP-Q------------------\n+-------------------------GRERYYSVVGYICE-TDTFGNNRRI\n+NEISEGDILCFKNAGAYCFTMASNYNSRYRPAEVLWHDDKAHLIRERETF\n+DDLI--------------KNQVDVKDLFVPEKVKVAV-------K\n+>688270.Celal_0333\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M--T-NHDLLNI--A--KTY--------------\n+--------------------------------------------------\n+------------GDPVYVYDSEKIIAQFNRLTNAFSGVKKLKLNYAAKAL\n+SNITILKLMNSLGSGLDTVSIQEVQLGLL--AGFKPENIIFTPNGVSLEE\n+IEEAAKLGVR-INIDN---LS-ILEQFGSKFP-KVPVCIRINPHVM-AGG\n+NS-NISVGHIDSKFGISIHQIPHLLRIV-ELTQMHINGIHMHTGSDILDI\n+DVFLYASEILFETAKNFKE----LDFIDFGSGFKVPYKEGDIETNIEELG\n+SKLTEKFNA-FCKEYGKELTLAFEPGKFLVSEAGQFLAKVNVVKQ-TTST\n+VFASIDSGFNHLIRPMLYGSYHQIENISNP-E------------------\n+-------------------------GRERYYSVVGYICE-TDTFASNRRI\n+TEISEGDILTFKNAGAYCFTMASNYNSRFRPAEVLWHKGEAVLIRERETL\n+EDII--------------KNQVDVKNLFSKKEKATA--------K\n+>867900.Celly_0105\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------M--Q-ASDLLKI--A--KTY--------------\n+--------------------------------------------------\n+------------GDPVYVYDSEKIVSQYQRLTNAFKGVKKLKLNYAAKAL\n+SNISILRLMNSLGSGLDTVSIQEVELGLL--AGFKPESIIYTPNGVSLEE\n+IEKAAALGVR-INIDN---LS-VLEQFGSKHP-NIPVCIRINPHVM-AGG\n+NS-NISVGHIDSKFGISIHQIPHLLRIV-DLTKMNINGIHMHTGSDILDI\n+DVFLYASEILFETAKNFKN----LDFIDFGSGFKVPYKTGDIETNVEELG\n+QKLSAKFND-FCKEYGKELTLAFEPGKFLVSESGFFLAKVNVVKQ-TTST\n+VFASIDSGFNHLIRPMLYGSSHEILNISNP-E------------------\n+-------------------------GRERYYSVVGYICE-TDTFASNRRI\n+NEISEGDILCFRNAGAYCFTMASNYNSRFRPPEVLWHNGEAILIRERETF\n+DDLI--------------KNQIDVKNLFSKKEMKKEK----ATAK\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,3184 @@\n+>760192.Halhy_3100\n+--------------------------M-AGEK-I----IFSMEGVSKTFP\n+P-TKQVLKNIWLSFFYGAKIGVLGLNGSGKSTLLKLIAGLDS--NYQGRI\n+TFDGNYKIGYLEQEPTLDESKTVRQIVEE-AVSEVVTKMAEYEEINLKLA\n+---EPMDEDEMMSLIEKQGELMEYLDHANAWELDHKLETAMDALRCPEGD\n+ALIKVLSGGERRRVALCRLLLSN-----PDILLLDEPTNHLDAESVDWLE\n+QYLQNFPGTVIAVTHDRYFLDNVAGWILELDRGEGIPWQGNYSSWLEQKA\n+KRLEQEEKTESKRRKTLERELEWIRLAPKARQAKGKARLSAYDKLADEEV\n+KEK----EAKLELFIPPGPRLGDVVIDVDNISKSFG-D-R-----ILFEN\n+VSFSIPKNAVVGIIGPNGVGKSTLFKIIMGKEKPDAGTVTIGDTVQLSYV\n+DQSHDQLKDGNKLVYDAISGGNDNIT-V--GKAVINSRAYISKFNFSGDA\n+QQKKLSFLSGGERNRVHLAMTLREGGNVLLLDEPTNDIDINTLRSLEDGL\n+ESFAGCVLVISHDRWFIDRLATHILSFEGDSTVEFFEGNYSDYEKVKKER\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------H-GDVTPKRPKFKNVINR------\n+>926562.Oweho_0933\n+--------------------------MSDDKK-V----IFSMSGVTKTYS\n+SNNKTVLKNIYLSFFYGAKIGILGLNGSGKSTLLKIIAGLEK--NYQGDV\n+VISPGYSVGYLSQEPELDESKTVIDIVKE-GAQETVDILAEYNKINDDFG\n+LPEVYEDPDKMEKLMARQAELQDKIDATNAWELDTMLNRAMDALRCPEPD\n+TPISVLSGGERRRVALCRLLLQQ-----PDILLLDEPTNHLDAESVLWLE\n+QHLQQYKGTVIAVTHDRYFLDNVAGWILELDRGEGIPWKGNYSSWLDQKT\n+KRLAQEEKQESKRRKTLERELDWVRMGAKGRQAKGKARLNNYNKMLSEEQ\n+RDK----EQKLEMFIPNGPRLGSNVIDANHVKKAFG-E-K-----LLYDD\n+LNFSLPPAGIVGIIGPNGAGKTTIFKMIMDQLEPDAGTFDVGETVKISYV\n+DQSHEDLK-PEKSIYEIISQGNEEIE-V--GNQKLNARAYLSRFNFAGQD\n+QSKKVGVLSGGERNRLHLAMALKEGGNVLLLDEPTNDLDVNTLRALEEAL\n+ENFAGCAVIISHDRWFLDRVCTHILAFEGDSQVYYYEGGFSDYEENKKKR\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------LG-DIAPTRVKYKKLIKNG-----\n+>1041826.FCOL_02765\n+--------------------------MSDDKK-V----IFSMSKVSKTYS\n+STNKQVLKDIYLSFFYGAKIGILGLNGSGKSSLLKIIAGVDK--NYQGDV\n+VFAPGYTVGYLEQEPQLDEEKTVIDIVRE-GAAEAVKLLEEFNTINDQFG\n+LPEVYENADKMQKLMDRQAELQDKIDACGAWELDNKLEVAMDALRCPDAD\n+TPIKVLSGGERRRVALCRLLLQE-----PDVLLLDEPTNHLDAESVHWLE\n+QHLQQYKGTIIAVTHDRYFLDNVAGWILELDRGEGIPWKGNYSSWLDQKA\n+KRLEQEEKTESKRRKILERELDWVRQGAKGRQTKQKARLQNYDRLLNEDS\n+KQL----EEKLELYIPNGPRLGTNVIDAKNVAKAFG-D-K-----LLYDN\n+LNFTLPQAGIVGIIGPNGAGKSTIFRMIMGEQQADSGSFEIGETVKIAYV\n+DQTHKNIN-PEKSIWENFCDGQELIM-M--GGRQVNSRAYLSKFNFSGSE\n+QNKKVAALSGGERNRLHLAMTLREEGNVLLLDEPTNDLDVNTLRALEEGL\n+ENFAGCAVIISHDRWFLDRVCTHILAFEGDSQVYYFEGGFTDYEENRKKR\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------LG-DLVPTRIRYKKLVR-------\n+>1034807.FBFL15_1199\n+--------------------------MSDDKK-V----IFSMQKLSKTYS\n+SSDKQVLKNIYLSFFYGAKIGILGLNGSGKSSLLRIIAGVDK--NYQGDI\n+VFQPGYSVGYLEQEPQLDESKTVIEIVRE-GVAETMAILDEFNTINDSFG\n+LPEVYENADKMQQLMDRQADLQDKIDALGAWEIDTKLEIAMDALRTPDAD\n+TPIKNLSGGERRRVALCRLLLQQ-----PDILLLDEPTNHLDAESVLWLE\n+QHLAQYSGTVIAVTHDRYFLDNVAGWILELDRGEGIPWKGNYSSWLDQKS\n+NRMAMEEKVASKRRKTLERELEWVKQGAKGRQTKQKARLQNYDKLLNEDQ\n+KQL----DEKLEIYIPNGPRLGTNVIEAQGVAKSFD-D-K-----LLYDN\n+LNFTLPQAGIVGIIGPNGAGKSTIFKMIMNEEKPDNGSFAIGDTVKIAYV\n+DQSHSNID-PNKSIWENFADGQELIM-M--GGKQVNSRAYLSRFNFGGSD\n+QNKKVSMLSGGERNRLHLAMTLKEEGNVLLLDEPTNDLDINTLRALEEGL\n+ENFAGCAVVISHDRWFLDRICTHILAFEGNSEVYFFEGSFSEYEENKKKR\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------LGGDLTPKRIKYRKLIRD------\n+>402612.FP1764\n+--------------------------MSDDKK-V----IFSMSKLSKTYQ\n+GADKQVLKNIYLSFFYGAKIGILGLNGSGKSSLLKIIAGVDK--NYQGDV\n+VFAPGYTVGYLEQEPILDDSKTVIEIVRE-GVAETMAVLDEFNKINDMFG\n+LPEYYEDADKMDKLMDRQAALQDKIDSLGAWEIDTKLEIAMDALRTPEAD\n+TPIKNLSGGERRRVALCRLLLQQ-----PDVLLLDEPTNHLDAESVLWLE\n+QHLAQYAGTVIAVTHDRYFLDNVAGWILELDRGEGIPWKGNYSSWLDQKS\n+SRMALEEKVASKRRKNLERELDWVRQGAKGRQTKQKARLQNYDKLLNEDQ\n+KQL----DENLEIYIPNGPRLGTNVIEAKNVAKAFG-D-K-----LLYDN\n+LNFTLPQAGIVGVIGPNGAGKSTIFRMIMGEQETDSGEFLVGETVKIAYV\n+DQSHSNID-PNKSIWENFSDGQELIM-M--GGRQVNSRAYLSRFNFGGGE\n+QNKKVNTLSGGERNRLHLAMTLKEEGNVLLLDEPTNDLDVNTLRALEEGL\n+ENFAGCAVVISHDRWFLDRICTHILAFEGDSEVYYFEGGFSEYEENKKKR\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------LGGDLTPKRLKYRKLIR----'..b'RWLELSEFA-----\n+>880070.Cycma_2011\n+-------------------------------M-N----YLSVDTLSKSF-\n+-GERVLFSEISFGIAQGQKTALVGINGAGKSTLMKIIMGEEI--ADAGQV\n+VINQEIKMAYVHQNPVFAGEKSIYQTIFDDPDNEIIQVIHEYQALMLKAE\n+GGEDN--SEALQP-------IFEKMDRLQAWDFEYQINEVLGKLGLHDTG\n+LQVSALSGGQRKRVAIARAILHF-----PDLLLLDEPTNHLDLETIEWLE\n+EYLSKSNLSLLMVTHDRYFLDKVTNNILELENGELYRYAGNYSYFLEKKA\n+ERKANQATEQEKAKSLYKKELDWIRRQPKARGTKAKYRVEAFNDTKEKAF\n+KKQ----EERDISLEVTAQRLGKKIVEIEKIHKSYG-D------LKLIED\n+FSYTFKKGDKVGIVGPNGAGKTTFLNMLIGKNDPDKGSVTIGQTTAFGYY\n+KQEEDSFD-ETLRLIDIVKEVAEVVT-V-AGGATITVSQFLTQFGFPPKQ\n+QHTHIAKLSGGERRRLQLLLILVKSPNFLILDEPTNDLDIVTLNTLEEFL\n+DVFPGCLVIVSHDRYFMDRLVDHLFVFEGNGQISDFPGNYTDLREKQKAA\n+KAEAPK-----QG----A-------------------EKKPV-A------\n+------A----K--TSEKE-STKATFKEKKEFEEISATLEQLTAKKDTYI\n+QKI-NQGTENHEELMEWSIEIEGLDEKIEALEMRWLELSELDGI--S\n+>388413.ALPR1_03480\n+-------------------------------M-N----YLSVENLSKAF-\n+-GERKLFSNISFGISQGQKIALVGINGAGKSTLMKIIMGLEI--PDTGQV\n+GINQQVKVAYVHQNPVFEGSLSIYQTIFDQSNSEVLQVIEDYHKAMLEAE\n+RGIDN--SDQMAT-------LFEKMDAFQAWDFEYQVKEVLGKLGLHDTD\n+LPVGTLSGGQRKRVALAKAILEK-----PDLLLLDEPTNHLDLETIEWLE\n+DYLAKANLALFMVTHDRYFLEKVTNEILELDQGKVHRYLGNYGYFLDKKA\n+ERMEIEDIELEKAKSLYKKELDWIRRQPKARSTKAKYRVDAFEETKEKAS\n+QKR----EERDIQLTVTTQRLGNKIIEIEKMKKSFG-D------KNIIRD\n+FSYTFRKKDRVGIVGPNGAGKTTFLNMITGQLAPDSGKISIGQTTAFGYY\n+RQEESSFD-EEKRLIDIVKDVAEVVN-I-AGGATITVSQFLTQFGFPPKQ\n+QHTPIAKLSGGERRRLQLLMVLIKNPNFLILDEPTNDLDLMTLNTLEEFL\n+DTFPGCLIIVSHDRYFMDRLVEHLFVFEGEGEIKDFPGNYSEFREWEKEN\n+KNQDSS-----RK----IQ--EPENK--I--------VDTKNEA------\n+------S----T--PLSQT-KAKASYKQKQEFKEVNTSISKLEKEKADIT\n+DKI-SAGIDDHEELIKQSNRIAEIDAELEELELVWLELSELDGI--E\n+>504472.Slin_4406\n+-------------------------------M-N----YLSAENLSKTY-\n+-GDRTLFKNLTFGINRGDKVAIVGANGSGKTTLLSILAGAMP--PDAGLV\n+SHRKDISIGYLDQQPDFNDALTVMEVVL-AGESAQLDAVRAYEHALAH--\n+---ED--NKGLEQ-------AMADMEKLEAWDYEAQIRQILGELGIQDFE\n+QIVGSLSGGQRKRVALARVLIQN-----PDLIILDEPTNHLDLEAIEYLE\n+NYLNTNNGTLLMVSHDRYFLDRVCNQIAEMDNGQLYTYKGNYAYFLEKKD\n+EREAAAASELTKDRNTFRRELEWMRRQPKARGTKAQYRIDAFEDLKEKTS\n+GKK----NDGDLDLNLRMARLGSKILEVENLSKRFG-E------KVLLDH\n+FTYTFKRPDRVGLIGKNGMGKTTLMNMLTGQLRPDSGKISTGGTVKFGYY\n+TQTELDLP-ENQRVIDVVQDVAEVMK-L-ANGDTITATQLLSRFLFDRSK\n+QYDFVAKLSGGEKRRLQLLLVLVQNPNFLILDEPTNDLDITTLNVLEDFL\n+INFPGCVLIVTHDRYFMDRLVEHVFVMEGEGKVRDYPGNYTDYREWRDSQ\n+PKANAR-----PG----KP--ATADV--K-------------SQATAPVV\n+--S-SVP----T--NQNGA-KRKLSFKEIREYETLEKDIESLEQRKTEIV\n+SLL-NTG-GHHEQLIAWSREIEQIDQTIAEKSDRWLELAEYI-----\n+>761193.Runsl_2861\n+-------------------------------M-N----YLSAENISKSF-\n+-GDKWLFKDLTLGLSRGDKMALIGANGTGKTTLMTILAGVTP--LDKGSV\n+SVRKDIRVGYLEQAPDFDGQLPVLEVLF-SGNNPVAKAVKEYEEALLS--\n+---GD--DKRFAA-------AIEKVDSLQAWDFEARVKEILGKLGIPDVT\n+VKIGTMSGGQRKRVALAKVLIES-----PDLLILDEPTNHLDLSMVEWLE\n+NYLNTQNTTLLLVTHDRYFLDTVCNVIVELDNGSLYTYKGNYAYFLEKKA\n+EREAIEASEVDKARNLYRKELDWIRRQPKARGTKAKYRVDAFEDTKEKAS\n+QRK----FDNQIELNVKSARLGSKIVELHSVGKRFG-N------RTVVNN\n+FLYTFKKGDRIGIVGKNGAGKSTLLNMITGELRPDNGQVVRGDTVQFGYY\n+KQTDLEYK-DGQRVVDWVKDVAEVIR-L-GTGQTVTASQYLNAFLFPPHK\n+QGTLIEKLSGGEKRRLQLLRILMAEPNFLILDEPTNDLDITTLNILEEFL\n+MNFPGCLIIVSHDRYFLDRLVDHLFVFEDSGNIRDFPGNYTDYRNFLAEN\n+NDPKND-----AK----TQ--ATTAS--A-------------KS------\n+------E----T--PAAPT-KRKLSYKEQKELESLEHEMAALEKQKAIFI\n+EKL-NGGSGSHEELTQWAKEIEQLNAKMEEKEMRWLELSEMG-----\n+>471854.Dfer_4068\n+-------------------------------M-N----YLSAENIAKSF-\n+-GDRWLFRNISFGISKGDKVALIGTNGTGKTTFLNILTGKIP--ADEGEV\n+SIRKDIRVGYLDQSPAFDESLPVLEVIF-SSNNPVAQVVKRYEHAIET--\n+---DN--HDELAQ-------VMEDMDKYNAWDFEYRTKEILGRLGIHHTD\n+NAYGTLSGGQRKRVALAKVLLED-----PDLLILDEPTNHLDLDTVEWLE\n+EYLNTSNTTLLVVTHDRYFLDTVCNQMLELDHGSAYSYKGNYSYFLEKKA\n+EREELEAATIDKARNLMRKELDWIRRQPKARGTKAKYRIDAFEDLKEKAS\n+QKK----FDVQMELNVRTSRLGSKIIELENISKGFG-E------RELIKN\n+FEYTFRRGDRIGIVGKNGMGKSTLLNMITGELQPDKGKISTGETVQFGYY\n+KQSDLVFN-ETQRVIDIVKDVAEVVQ-L-GTGETVTVGHLLQAFLFSPSK\n+QYDFISKLSGGERRRLQLLLILIKQPNFLILDEPTNDLDIDSLNVLEEFL\n+LNFPGCLMIVSHDRYFLDRLVEHIFVFEGEGKISDFPGNYTELRDYQDEQ\n+EAEKKL-----AA----AN--AAAKP--A-------------AKELAQPK\n+--E-PVA----V--PAAAA-KRKLSYKEQKEMEQLESDIAKMEETKAKLV\n+ENL-NNG-GSHEELAKWSKQIEEINESQADKELRWLELSENA-----\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,55188 @@\n+>471854.Dfer_2353\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------MKPGRCWKS--L-----------LLC---I\n+-QLL---A-G----WV-----H----AQ-------------------D--\n+--R--V-FEVNQ----------------------Y---------------\n+-DER-------------Q-----------------GLSSRLV--------\n+-----------------------HC-MIQDKKGFL-WLGTSD-GLNRYDG\n+HGF----ITFRSS-------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------A--------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------DNP-KS--M-A-GNYIT--AL-AEDL-N-GNIWVGF-Y\n+TGG-IS--CY-NPVR-GQ--FT--------NYEMTDVQG--RD-------\n+LSG------E-----EVKML--Y-ID-R--QN------------------\n+---------------------TVW----------TSIK--GEGLIRL---\n+----D---QA-G--G-K------HRQ--YNIV-------ET-------AT\n+G-IN-------------------QPE--YRKAFNIVYR-VY-E-QP---G\n+G-RFYLL-------------------TH---T-G-LY--------L----\n+------FNKTSG--------------------------------------\n+--------------------------------------------------\n+N-L-----------------------------------------------\n+-------NA-------------I---------------------------\n+-PDPDA-S-G-HL---------------V-PQ-N-LF-ISY----T----\n+--VEDDVLW---LGSWA-----GG-L-----------AAF--NIK-T---\n+GG---W-K-------------RY--------------R-F-D-----P-R\n+--------------I--LP-TTN-IIS-GIH-----HSG---SDTLWLTS\n+I---DR------------GFG-------YF---------DK----K----\n+------K---EE---FV--FLA-G--K----------------Q------\n+-----------------GFP---TGSYNG--LLADRENN-LWLN--TE--\n+--NML---VA------------------------AF--RQS--K------\n+-PF----TFVPVNV---KK---RD--HS--V---FHSITSII---E-DDH\n+F-KLTATL---WA------DGL---QV--HNKKT---------G--VTKA\n+LGVDT-H-----M--DE-P--LQR--------------V-N--N----IW\n+K--D-K-----S--GTVW--------------------------------\n+-------------------VI-S---------RDV--IYT---FD-----\n+PV-R----------------------------------------------\n+-----------------------------------ET-------LV----\n+-KIP-----Q----------------------PPAWT-----AE-K---P\n+S--N-FF----LS---IRQD----K-A---N-TFWIA----T-A-R-N--\n+---GL-FRYD-PR---NA-------KY----------T------------\n+-HY-APS-A--T-R--------------P-I--ATRLISAI---DTDEYG\n+-TL-----------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------WVA-\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------GKNG-YLA-------------------------------\n+-------------------------------------------------F\n+Y-D----------QKQDA---------------F---------LP---V-\n+-P------------------------------------------------\n+-VAYKDRK-A-K-S-VSSVF-----CQ---P-G--GRLYVGT--------\n+---------------------------------------E--L-G-LL--\n+-------'..b'----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------MV-----NNS-I-\n+----QSII---EDDK---QQIWVA-TS-----------------------\n+-------N--GLSCVHI-------------------SE-E-----K--K-\n+------DP--A----------FFFTN-YNQYD------G-----------\n+--------------------------VV-D---YEF--------------\n+-----V-KN-S-V-L--------KM-N-----------------------\n+----------------N---------------------------------\n+-------GSLLW-------------------------------GGLD-GF\n+NIFN----P-ANN-L-LE--------------------------------\n+-----------K------------T-----K--L-E-VPIFTQFEL----\n+FGK--PI-SP------G--Q-E----------------FNGKTI-L-DK-\n+-------AIQ-------Y--T-S-A-----------ITLK-------HRQ\n+--NFFSLS-----FS----GL-NYTN--VS--------------------\n+------KT----KYKY-RLEGI------D--EN------------WQ-EI\n+-APDN--G-L-----------------------------------GKAS-\n+--YTDLS-PGD--------YTLKVT---SSA---N-G---T-I-------\n+-------------------------------W-S-D---M----------\n+---ATLHIIIL-PPW-WKT--W-PA--YLGY-I--V---L--ILFIIYLC\n+--F---HL------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------LLK-Y----\n+-Q--K----------------EK-----------L---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------K---------------------A--\n+KQ--SEELR----TLKDQFFTNVSHELKTPLSLIITP-LASI-L-K----\n+--------T-E-----------N---------SSNRSKLTKIHQSA-IEL\n+LQLVNQLLDVRKIETTGKL-SVNSDCCQLNQLLNN---------------\n+VTQ-------------------PF--D-ELAQHKGIRFKR-EI-S--K--\n+-----------EE--T-LIFID-NEKFKKIVSNLLSNAFKFTPQ-EGK-V\n+--SFI--GE-------------------------------------LDG-\n+EIL-----KIQV-TD-NGKGIAKEEVP--KIFE---RY-YRSN--P----\n+-------E-GE-N-TGTGIGLHLVKSYLE-LLGGTVNV-T-SAP-A----\n+----KGSTFTVRIPV--RIN-IP---------------------------\n+-----AQ-----PK------------------------------------\n+------------------I-LT---S------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------Y----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------K-D-T----N-------EGF\n+S--ILIVED-HPDFQDFLFSEL---KED-FNI--YTAKNGLEGLEQV---\n+-K-K--H-HP-DLVISDIM--------------------MPV-MTGITLC\n+HNIKSD-IEISHIPVILLSARS-S-EE-SKLKGFEAKADAYMDK-PFNLE\n+ILKQRIENL--V--Q---EQQ--------SR--KEVF----------KN-\n+-------S------A-----------------------------------\n+----------------E-------I---------------------K---\n+-------------P-------D------------EIT-I---G----K--\n+--------------------------------------TD-------SL-\n+--------FMEKALQKVHENM----EN-----------------------\n+------------------------------------------------TA\n+----------YSVKQLSS-----------------DLN--MDRT------\n+GLFRKI---------KAITG----------------------------LS\n+PTA---------FIRSIKL---KH-----ARQ-LL-DE------------\n+--------------------------------------------------\n+------------------GKSV-SEVSVKVGF------------------\n+SSLS--------------YFGKCFQ-------------Q-E--YGKK---\n+-PSDYK-N------------------------------------------\n+----\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,354 @@\n+>518766.Rmar_1965\n+MQNFARPDHERGATTMEARPVRLSRCVMTEIVIPNDLNGLGNLLGGRLLH\n+WMDLCAAISAQRHTNRV-CVTAAVDFVEFRSPIRQGEIVVLESQVNRAFR\n+TSMEIEVNVWAEDP-RTQSR-RFCNRAFYTFVAVDE-EGRPVPVPPVKPE\n+TPEEQERYEQAARRRELRLLLSGRLPAEKARRLQA-SLAELAASASESPE\n+TNS\n+>309807.SRU_1852\n+-----------MSSPRSPKPVSASKCKMTEIVLPNDTNGLGNMMGGRLLH\n+LMDKCAAISAQRHANRV-CVTAAVDSVEFQSAIQEGEVVVIESHVNRAFR\n+TSMEVELNVWAENP-LEETH-RTCNRAFYTYVALDE-DGGTVPVPDVSPS\n+TEQEQDRYEAAAKRRDIRLVLAGRKDLEDAASLKEDMLTALQHSTDA-PA\n+---\n+>760192.Halhy_6370\n+------------MQTLEPKRVTESRSVMTEMVMPNDANPMGNLMGGNLLR\n+WMDIASAICAGKHCERH-VVTASVDHVSFQRPIKVGDVVTLEATVTRAFN\n+SSLEVYVEVFAADI-KGQNA-RRCNHAYYSFVALDDANGSPISIPPVIPL\n+TEIEQNRYDSAPRRREIRLILSGRMKPEDATDLKDF-FKQFSNK------\n+---\n+>755732.Fluta_1652\n+---------------MKPRNASETLAITTKVVLPNDTNTLGNLFGGQLLA\n+WMDEIASVSAHRHSRRV-VVTASVNNVSFNSPINHASIVTLESKVSRAFN\n+SSMEVFVDVFVEDH-ITGKR-SKSNEAIYTFVAVD-QNGGPIQVPELIPE\n+TEEEIERFEGALRRKQLALILAKKMSPKDATELRKL-FTE----------\n+---\n+>926562.Oweho_2156\n+---------------MKAKTPKDSLTIFTEIVLPNDTNNLKNLFGGQLLS\n+WMDRASAVAAHRHCKRI-VVTASVNNVSFAHPIPQGAIVTLEAKVSRAFT\n+SSMEVIVDVFVEDQTVAGKK-IRANEAIYTFVAVD-QLGNPINVPELIPE\n+TDLEKQRHEGALRRKQLSLIIGGKMKPEDATELKAL-FFPEDADSKQDA-\n+---\n+>992406.RIA_0615\n+---------------MTKKTPKDSLTVMTNIVLPNETNHLGNLFGGELLS\n+KMDRCASISASRHCGRR-VVTASVNHVSFNHPIPEGGVVVLESKVTRAFS\n+TSMEVYVDVWMDDP-ITQKK-VHTNEGIYTFVAVD-AFNKPVPIPELEPE\n+TDIEKERYMAALRRKELSLILSGRMKAQDSVELKKL-FI-----------\n+---\n+>531844.FIC_00156\n+--------------MGKIKTASESLTVMTNIVLPNETNSLRNLFGGELLA\n+KMDRCASISAARHCERR-VVTASVNHVSFNFPIPEGGIVVLESKVSRAFS\n+TSMEIYVDVWLDDP-INQTK-THTNEGIYTFVAVD-EFNRPIPIPQMEPE\n+TEEEILRFDAALRRKELSLIFSGRMKAADSVELKKL-FSAV---------\n+---\n+>525257.HMPREF0204_11045\n+--------------MAKIKKASESLTIMTNIVLPNETNSLRNLFGGELLA\n+KMDRCASISAARHCERR-VVTASVNHVSFNHPIPEGGVVVLESKVSRAFS\n+TSMEVYVDVWLDDP-INQKK-VHTNAGIYTFVAVD-EFNRPIPIPEMIPE\n+TDEEKERFAAAFRRKELSLILSGRMKPLESVELKKL-FQEPQESKKDKK-\n+---\n+>865938.Weevi_0914\n+--------------MLKSKTAKESLAIMTNLVLPSEINALNNMFGGELLA\n+RMDRISSIAARTHAGSYQVVTASVNHVSFDRPIPLGSTVRLEAKVTRAFS\n+TSMEVYVDVYLYDY-KNSCY-EKTNNGIYTFVAVD-ENNKPTRVPELIPE\n+TEQEIERYEAALRRKQLSLVLGGRMKPEEAHELKAL-FS-----------\n+---\n+>888059.HMPREF9071_2061\n+------------MKNLEPKTVAFSRSVSTDLVLPNETNHYGNMFGGELLA\n+RMDRVGTIAAVRHSGNV-VVTAAVNSVSFNKTIPQGSMVTVEAMVSRAFT\n+SSMEVYIDVWVEDP-ENGNR-VKSNEAIYTFVALN-KAGQPVEVPQVIPE\n+TSLEIERYQGALRRKQLSLVLAGRLKPHDASELQDF-FQDLEHQ------\n+---\n+>553178.CAPGI0001_0595\n+------------MNNLAPKKVSESRSVSTDLVLPNETNHYGNMFGGELLA\n+RMDRVGTIAAVRHSGCV-VVTAAVNSVSFNKTIPQGSVVTVEASISRAFT\n+SSMEVYIDVWVEDS-VSGER-IKSNEAIYTFVALN-AEDKPVAVPEIIPE\n+TDLEKERYEGALRRKQLSLVLAGRIKPHEASELQSL-FQDLENQ------\n+---\n+>313598.MED152_10705\n+---------------MEAKTPRESLTILTDLVLPGDTNYLDNLFGGELLA\n+RMDRACSIAARRHSSRI-VVTASVNHVAFNKSVPVGSVVTLEAKVSRAFK\n+SSMEIYVDVWIEDR-QSGMR-TKVNEGIYTFVAVD-ETGKPVQIPQIVPE\n+TELEKIRFDGALRRKQLSLVLAGKMKPDEATELKAL-FKS----------\n+---\n+>313594.PI23P_05152\n+---------------MEAKTSTASLTILTDLVLPGETNYLDNLFGGELLA\n+RMDRACSIAARRHSRRI-VVTASVNHVAFNKSVPVGSVVTVEAKVSRAFN\n+SSMEIYVDVWIEDR-QSRHR-TKVNEGIYTFVAVD-ETGKPVKIPELIPE\n+TPLEKERFEGALRRKQLSLVLAGKLKPNEATELKAL-FN-----------\n+---\n+>156586.BBFL7_01464\n+---------------MEAKTPSQSFTTVTDMVLPSETNPLNNLFGGELLA\n+RMDRAASIAARRHSRRI-VVTASVNHVAFNRMVPLGSVVTIEAKVTRAFT\n+SSMEVHMNVWIEDR-ESGEK-TQANEAIYTFVAVD-ETGRPVQIPAILPE\n+TEDEKSKYDAALRRKQLSLVLAGKMKAKDATELKAL-FED----------\n+---\n+>50743.SCB49_05552\n+---------------MEAKTPSASCTVITDLVLPSETNPIGNLFGGELLA\n+RMDRAASIAARRHSRRI-VVTASVNHVAFNKMIPLGSVVTVEANVSRAFT\n+SSMEVYMDVWIEDR-ESGVK-SKANEGIYTFVAVD-EMGSPVPVPPIIPE\n+SALEKERFDAALRRKQLSLLLAKKIKPEDATELKAL-FE-----------\n+---\n+>216432.CA2559_03525\n+---------------MEAKTPKESKTTYTDLVLPSETNPLNNLFGGELLA\n+RMDRAASISARRHSRRI-VVTASVNHVAFNRSIPVGSVVTVEAIVSRAFR\n+TSMEVFIEVYVEDR-ESGLR-SLSNEAIYTFVAVD-DLGSPVAIPPLKPE\n+TDLEISRYDAALRRKQLSLVLAGKMKANDATELKAL-FED----------\n+---\n+>313590.MED134_09616\n+---------------MDSRTPSDSKTILTDLVLPSETNPLGNLFGGELLA\n+RMDRAASIAARRHSRRI-VVTASVNHVAFNRMIALGSVVTVEAKISRAFK\n+TSMEVIIDVWIEDR-ESGLK-TQANEAIYTFVAVD-EQGQPVPVPQVVPE\n+SDLEKQRYDAALRRKQLSLVLAGKMKPAEATELKAL-FI-----------\n+---\n+>9'..b'GKLSPHDATELKAL-FTELENS------\n+---\n+>269798.CHU_1929\n+-------------MNPQARHPSESMVIKSELVLPNDTNTLNNLMGGRLMY\n+LMDVVGAICALRHCSHG-VVTASVDNVSFKAPIALGNILTLEAKITRAFH\n+TSMEVHIEVWAEDV-LSRVK-TKSNEAFFTFVALS-ADKKPLPIPEVIPE\n+TEREKELYAGALRRRQLRLILAGRMKPSEATELKAL-FENL---------\n+---\n+>700598.Niako_4655\n+-------------MDQFSKTAKESVVTMTELVLPNDTNMFGNLMGGRLMY\n+WMDIAAALAAMKHCGTP-VVTASVDNISFENPIKLGNAVHIQARVSRAFN\n+TSMEIFMSVWGEDA-LHQYK-YKSNEAYFTFVALD-PNGKPRKVPNLLPE\n+SEEEKELFEGALRRRQVRLILGGKMKPDDATELKAL-FKL----------\n+---\n+>485918.Cpin_6613\n+-------------MTLTPKRAQDSVIQMTELVLPNDTNTFGNLMGGRLMY\n+WMDIAGALATMKHCSAP-VVTASVDNISFETPIKLGNVVHIEAKVSRAFS\n+TSMEVHLRVWGEDP-VQQYR-YKSNEAFMTFVALD-PNGKSRLVPQIIPD\n+TEEEKQLYEGAMRRRQLRLILSGKMKPQDAEELRAL-FL-----------\n+---\n+>525373.HMPREF0766_12235\n+---------------MKSKTAKESYMVMNELVLPNDTNTFNNLMGGRLLY\n+WMDICSAMAAQKHANSP-VVTVSVDNVSFKRSIKLGEVLTIEAQVTRAFN\n+TSLEVRMEVFAQNL-PLGTK-VKSNEAYYTFVAVD-EHTQPQPIPELIPE\n+TEKEHKLYDEALQRRELRLILAGKIKPQHATGIKKL-LKMLEQKD-----\n+---\n+>649349.Lbys_3048\n+--------------MPKAKYVKDSHTIMTEMVLPNDTNTLSNLMGGNLMR\n+LVDIAGAICAQKHSNRI-VVTASVDHVSFVNPIPLGNVITLEAKITRAFN\n+TSMEVVVDVYSENI-PAGTK-KKTNQAFLTFVAVDQ-SGRPIEVSEAIPE\n+TEEEKLQFERALHRRQLRLLMAGRLNPEDTESLKQT-FFNSPTTI-----\n+---\n+>761193.Runsl_5592\n+--------------MPLPRKACDSHTIMTEMVLPNDTNTLNNLMGGRLLH\n+WMDICAAIAAQKHAHRT-VVTASVDNVSFAEPIKLGNIVTFEAQVTRAFT\n+SSMEVHIKVSAQNI-SAGEKAVHTNAAFYTFVAVD-QSGRPIEVAPVIAE\n+TEEEKQLFESALRRRQLRLVLAGRMNPAEAVELKAL-FGV----------\n+---\n+>471854.Dfer_4260\n+--------------MLKPKKPHQSEVTMTEMVLPNDTNTLNNLMGGRLLH\n+WMDICAAISAQKHSNRI-VVTASVDNVSFTEPIRLGNIVTMRAKVTRAFN\n+SSMEVFLEVWAEDI-PAGVR-VSTNRAFYTFVAVD-QNGRPIEVPPLEPE\n+TDEENELYLSALRRRQLRLVLAGRLNASEATELKAL-FKVE---------\n+---\n+>504472.Slin_0539\n+--------------MPQPKHARDSITVMTEMVLPNDTNTLNNLMGGRLLH\n+FMDIAAAIAAQKHSNRI-VVTASVDNVSFSEPIRLGNIVTMKAQVTRAFS\n+SSMEVFIEVWAEDI-PAGIR-VSTNSAYYTFVAVD-QSGRPIEVPAVIPE\n+TDDEKDRYASALRRRQLRLVLAGRMNPQDATELREF-LQV----------\n+---\n+>313606.M23134_07521\n+-------------MALNKKKASESLTTMTELVLPNDTNTLNNLMGGHLMY\n+LMDICGAIAAQKHSNRI-VVTASVDNISFKEPIALGDVVTIKAHVSRAFN\n+SSMEVYLEVTAGNI-PQGTM-RETNKAFLTFVAVD-QSGNTIMVPELVPE\n+TEKEVALFDGALRRRQLRLILAGKMKPNDATELKSL-FDSSPN-------\n+---\n+>880070.Cycma_0634\n+-------------MKESFKHVKDSVVTMTEMVLPNDTNTLNNLMGGKLMH\n+WMDVVAAIAAQRHSNSI-VVTASVDNISFKNPIALGNVVTLNAQVTRAFN\n+TSMEVYIEVFAEDI-PANSK-YASHKAFFTFVAVD-SEGKPVKVPELKPV\n+NGKEEELYKGALRRRQLRLILAKRMDPKDATELLAL-FDSEGIGQKE---\n+---\n+>388413.ALPR1_10820\n+--------------MPKKKFAKESATIMTEMVLPNDTNTLNNLMGGKLMH\n+WLDVVAAIAAQKHSNRI-VVTASADSISFKEPIALGNVVTLKSQVTRSFN\n+SSMEVFIEVIAEDI-PANKK-IMTHRAFFTFVAVD-QNGKPIEVPEVVPE\n+TPEEIEHFEGALRRRQLRLVLSKRMKPEDAVELKSI-FNLTEPK------\n+---\n+>762903.Pedsa_1084\n+--------------MLKAKKAKESLVVMSELVLPNDTNMLHNLMGGRLLH\n+WMDIAAGISAQRHCNNI-AVTASVDNVSFRNPVKLGDVITIQAKVTRSFN\n+TSMEVRITVYAENI-PSGSK-VKSNEAFYTFVALN-ENGVKTEVPELIPE\n+TAEEIALFNTAMQRRELRLVLAGKLKPSEASSIKSI-FN-----------\n+---\n+>643867.Ftrac_3096\n+-------------MPKQAKNPKDTYTIMTELVLPNDTNPLNNLMGGRLMH\n+WMDIVSAIAAQKHCNRI-VVTASVDNISFQHPIALGDVVTLEAKVTRAFS\n+SSVEVHIVVKGENI-PSGKK-YPSNSAFFTFVAVD-QSGRPIDVPELIPE\n+TEEEQELFDGALRRRQLRLVLGKRMKPEEATELKSI-FKLDE--------\n+---\n+>714943.Mucpa_4890\n+---------------MKIKTPQDSHTIMNELVLPNDTNTLNNLMGGRLLH\n+WMDIAAAIAAQKHCNRI-VVTASVDTVSFKHPVKLGDVISIESKVTRAFN\n+TSVEVRLDVWAQNI-PSGTR-IKSNEAYYTFVALD-EDSHIVSVPELTPQ\n+TEEDHMFYAGALRRRQLRLVLAGRMDPHDATELKAL-FFPEPI-------\n+---\n+>743722.Sph21_3539\n+---------------MNKKFAKESFTIMNELVLPNDTNTLNNLMGGRLLH\n+WMDIAAAISAQKHCNRI-VVTASVDNVSFRHPVKLGDVISIEAKVTRAFN\n+TSVEVQLQVYAQNI-PSGSR-IKSNEAFYTFVAID-QNSRTIAVPELVPE\n+TEEEKELFDGALRRRQLRLILAGKMKPEEASELYNF-FNQIGAK------\n+---\n+>391596.PBAL39_12618\n+-------------MSKKMKSAKDSFTIMNELVLPNDTNTLNNLMGGRLLH\n+WMDIAAAISAQKHCNRI-VVTASVDNVSFKQPIKLGDVITIEAKVTRAFN\n+TSVEVRLDVWAENI-PSGTR-MKSNEAYYTFVAVD-QSGRTIPVPELQAE\n+TADEIELYEGALRRRQLRLVLSGKMDAHDATELKAL-FFKD---------\n+---\n+>485917.Phep_1262\n+-------------MSIKIKSPKDSFTIMNELVLPNDTNTLNNLMGGRLLH\n+WMDIAAAISAQKHCNRI-VVTASVDNVSFQQPIKLGDVITIEAKVTRAFN\n+TSVEVRLDVWAENI-PSGSR-AKSNEAYYTFVAVD-QSGRTIPVPELKPE\n+TEAEKELFAGALRRRQLRLILGGKMKPNDAKELKAL-FFPEE--------\n+---\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,31844 @@\n+>525373.HMPREF0766_10806\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------------M\n+----------LK----------K-------YFS---I---L--F-LVWVW\n+--------------------------M-YAT-E-S---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------SAQT-H-------------\n+-------I-TLEGR-ILD-QK-S-DEP-ISGVSVSV---KENP-----RS\n+--G-----S-VI-TGSQGSFRI--------R-A---H-RG-Q------TL\n+--VISHIGYM--A---T------EAV-----V----NT----S-Q-SNLI\n+FR--LT----ED-P-H-ELSEVLV-------TGA-LGIKRQSRELGTSAQ\n+SVNNEELN-LG--KV--VNPLLALSSKVAGLRVNATDLTTGKTDPGIQIR\n+LRGTRSL------NR--S-KN--D-PLYVVD-GVPL--------------\n+--------------------------------------------------\n+----------PD-IT-R-INPNDIQDITVLKGANAAALYGSEGVNGAIMI\n+TTKSGR----------SERG-QINFSNSTTFSN---VFLLPPAQTVFGQG\n+QNGVY---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------SPVANESWG----DKFNG------E----T----R-\n+----DFG-------L-----------------------------------\n+----------PINGVQ----------------------------------\n+-----------PTKV--Y-----------S----A--P------------\n+----------S--------------------------K---D-N-RLGFF\n+DTGITAQNDLSFSGGD-E----KG--SYFVSLQDVRIKGVIP-G--D--K\n+S-SRTGARF--NGSR-R-FN---KLNTSFNMNYVFFKNNT-T----SD--\n+-----------------------------------------------G--\n+------P----------W-----L-SV----Y-TQPAN-----IDY----\n+KE------------------------------------------------\n+---ARN-WED---PASPNHPLNW---------------------------\n+---------------YN-----P---------------------------\n+----------------------------------------V-A-------\n+-----STRNP-I-FM--ADNN-RNM-YDQHTLNSKLEFNYEFT-DW----\n+--------FDATYRTGL-YFQSEPGRVT--------NRKLVSNVAT----\n+-------------------------------------------RN-----\n+----------------IN----GSV--NDTHRGFTRFNN-DLILNFH-K-\n+N--F-------------G-D------FSTKLLVGQNI--RMDD-S--KLI\n+-NV-SAA--------N--L------------------L----------F-\n+----EDIF-NQGSR--TG-E---------L---------------T----\n+-GG-S--T---ITKYRS-L-ATYGEFTAGYRNYLFLTLTGRNDQVSVL--\n+-D-----P-N------------------N-----N-SYF-SPGISSSFVF\n+TDA--IESL-K-------------NSS---I--LSYGRIYTSYNKT----\n+--GNVT------L--DPYR--------L--------N----------L-T\n+Y--SQ--------------TG----------------G--F---------\n+-PF----G----S--------L-----V--G----FT-------P-----\n+----SL-S-E-P--N--LLIKPEFVKSFEVGTQLAFFND----RLRTDIA\n+CAYSDSDGQIF-NAGISSAT---GF-NSTIVNAGQIINKTLEVMING---\n+T-AIK-----NR---D-VRLEFGVNFSY-TDTKAKNL--YA--G------\n+------------------------DEFN-------------I--------\n+-----------------F---RQA-----YAIKG-----LQYPTLRMT--\n+-D-F----LRE------------------------------------D-G\n+--KI-------------------------------------------VL-\n+DK------------------------------------------------\n+---D-------G----------N-V--IP------S--T------D----\n+---------------E---K---------VLG-TMVPPYLFGFNTKFS--\n+YKSLTVGFQIDSRLGSWMYSEVVPRMYAAGTHP-E-T-V-KY-DR--Q--\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------P--F--I------\n+----------M------PN---S-----------------MV--------\n+--------------------------------------------------\n+------------------------------------R-------------\n+--------LADGSIVENTNVYSK---G-----------------------\n+---DK--A----------W--W---------T------------------\n+------------AYGNI--QTTT-A--AKGDYLKLRELYIGY--DLPE-K\n+WL-T-G-QK--L--IKKASIGFVGNNLFIIRH-SSN--T-----I-----\n+-----GDPEA--LY--------N---------------------------\n+------------QTD-G-Y-N-SFRQI-PSARSMGFNVNMTF-\n+>525257.HMPREF0204_11830\n+---------------------------------'..b'F--T--N---S-G-------------------G--------\n+------------NV-QG-I-E-GGN-I-PTPVTYGFNVNLKF-\n+>485917.Phep_3384\n+---------------MIFYLNVKRG-GNHSIKRK-LI-M------RIN--\n+------L-------S---------------------------I-------\n+--------FF----------------------I-----------L-----\n+----LAM----IQ-----------V-------------SARE-------V\n+FAQKI-T--LDR--TNS---SLNQLIKDIRSQ------------------\n+----------------------SGYDFFYNNAVIVKA-RP---VSIH---\n+----------------------------VK-----N--------VSLDEA\n+LQKCF-------------------A------------N-----QSL----\n+--------------------------------------------------\n+------------T------YR-----------------------------\n+--------------------------------------------------\n+------------------------------IT-DKMVVI------ME---\n+----KE-N--H------------E-----A-APAV-Q-------------\n+-------Q-SVTGKV-VD-S-LG-M-P-LPGATIRV---KGS----S---\n+------R-V-TL-TDAKGVFVL------K-D-IA---D-N--A-----LL\n+--EISYLGFV--S---R--E--I--KA-----------S---P-NMG--N\n+IV--L---R-AS-Q-S-GLNEIVV------T---AMGISREKKALGYAVQ\n+DVKSEEL--TT--RP--TNALSAISGKVAGLQVISSG---GNMGGSTRVL\n+LRGINSI-M-----G----N-N-Q-PLYVID-GTPID-NSDI---NT---\n+-----T-------------S----------------T-I-D--G----S-\n+A-G--K-DVGNL-IQ-D-LNPDDIENISVLKGPSAAAIYGSRAANGVILV\n+TTKKGS--K-----K--EKF-DITLNTGVDLEN-V--VRLPARQHLYGQG\n+Y------------------AT--T------------------------F-\n+-------A----------------KA------------------------\n+-----T----IAGK--E-Y--N------------I---V--DYAS-D---\n+-----------ES--------WG----PKL--D--G--T----P-VL-H-\n+---W--YN------------------L-----------------------\n+------D----------------------------------P---E---Y\n+--PA---D--Y---L--N-----------P----Q--P------------\n+----------W-V---------Y-P------------E---H-D-VNYFF\n+RTGIANTNNIAISGAS-D----KT--TYRLSYTNKNVRGTVP-N--S--S\n+L-GRNAVNF--SGST-Q-LG---IVNVFSNLNYIKNTSLGRP----W---\n+--T--G-A--S-------N-------------------------------\n+-RN---I----------M-----L-E-AF--Q-WGGVQ-----VD--Y--\n+KK---LS----E----------------------------YK--------\n+------R---P--SD------------------------------G----\n+-T------------PRA------------------------WN-R---S-\n+----S------------YLNTPAG---K-----A-----------T----\n+R----FIDNP-Y-WS--AYES-YLE-ENRDRLYGNIGFTVDAN-N-W---\n+--L------KLTGKVHADIYTFEYQDRIA----V-Y-----S--------\n+--------R-----S-Q---------------------------------\n+----------------------SQY-Q-EYNNHFNEFNY-EFLATAK-K-\n+N----W-------------D-D----FSLSGNVGGN--IRDQK-R-R-VI\n+-DG-L--T-Q-G---G--L------------------I----------V-\n+----PLFY-NLKNA--PN---V-------L----N----------N----\n+-N-----N---FYHRQV-Y-SLYGSFSAGWKGMLYLDGTLRNDWSSTL--\n+-P-----V------------N-------N-----N-SF-IYPSVTGSFVI\n+SELA------G---IKK-Q-------E---W--LDFAKVRLGWAQV----\n+--GND-------T--D--------PYQL--------Y------P-----V\n+F--EA--------------Q---Q------S------F------------\n+---N-S------N--------------P--S----Y-R------LP----\n+-----G-T-L-N--N--PDLKPEITSSVEAGLNVQLFKN----RLGFDIT\n+YYNNNSRNQILP-VPVSAAF---GY-DKKVLNAGKINNKGLEVTLNG---\n+T-PVK--------ST-NFEWNSTINWSR-NRNKVVSLD--R----G----\n+----V---------N---T-LE------L-----S----N----------\n+----L------------L---VTL-----VAQEG-----KPYGQIM--GY\n+--DF--V--YA----------------------------------P----\n+-------------------D----------------GQ--R------VV-\n+Q---------A----------------D----------------------\n+-----------G----------T-Y--LK------T--S----Q------\n+----------------L--V---------PL-GSVLPDYLFGFQNTFR-Y\n+-KKLRMGFLIDGRMGGSFFSQTYKVGMYSGVLD-R-TA-A----------\n+-----NG-------------------------------------------\n+--------------------------------------------------\n+----------------------------IRE-T-----------------\n+-------------------------------------G--T--V------\n+----------V---------D-GV-----------------K--------\n+-A------------------------------------------------\n+-----NV---V----FHPDGTYTVSNTSK-------N--E-----T----\n+-------R------------I---------------S------A-L----\n+-------N-------------W--------A-R----------NE-----\n+----Y---N-G--------PTTFSV-F-DASYIKLREVTLGY--NFDL-K\n+---K-T--G--T--IRSVGLTLYGRNLWNIYT----K-SK----------\n+--Y--IDPEF--T--N---S-S-------------------G--------\n+------------NV-QG-I-E-GGN-I-PVPVTYGLNVSVKF-\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,11320 @@\n+>553177.CAPSP0001_1787\n+--------------------------------------------------\n+--------------------------------------------------\n+----------M--KRILFLVM----------V------------------\n+--------------------------------------------------\n+-----------------------L---------L----------------\n+PLAI----------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------T---\n+H--AQSIYKGTLVSE---KGEPIFGANVIQL--TL--P-D-ST-M-VK-G\n+AISDDKGHFEL-P--DNA--Q--GKS--SVIK-----ITHLE-YKE-KV-\n+--LTPS--L-G----------------D-LGTISLQ--K--S------V-\n+-N-ELGEVVV--SA-HR---PVMKQQGTVITADVAASSLKN-IPKVDLLL\n+YFLPGVSMSYTS--YGVEVFGKGKPLFYINNKRVRDMN-------DVYRL\n+SPKEIDRISLETQPGAEYDNS-VGAVIHIFLKK--------K---QGDGL\n+SGGVSVES-------Q----F---KK-----------GQ-----------\n+EG-FVDAH--LNYRSGN-TD-VFFSTHA-------NVN-H-N-------F\n+KREN--S-Q--ELNVH----TQAN--------------------------\n+----------------N-WQ----VR-TNEIVKDNTRR-FYAKTGFSHE-\n+IND-----KHSLGASVWM-T-TSPL-S-GHNITE-QN-T--S--------\n+T---------YR-N--------GTLSQQG----LN--TFDRL-NK-----\n+-DT--RL-NANVYYD-G-KL--SDK--LK--LQTDVFYRGAFSNYRS---\n+-DII--ERN--LTT-------------P-----------SL-------RN\n+------I--NTHSD----AQSHLWTMKTNLT-QRV--G---K-------G\n+LLGYGVEASTLSRYDNYED-------------------------------\n+--------------NI-STPTDIDNKETQSAAFASYSF-PW-LKAKW--K\n+IGARYEYTDFGYFE--ND---------------------V-----K----\n+S------NV-K--------SRSY-KHLLPNISVAFPW-H--K-TEWSFSY\n+AKKITRPAFYELSDRFT-YETPFLYNRGNTDLQPRLSDDFSLLLT--Y--\n+------Q--I-VSLSVDYSLVHNGFFED-YQ-L-S-R-------------\n+----------------------TLPN----V---V-ER---------YIH\n+NFGDYQRL-RLELSAY-YQ-I-G------------R-WVPK-------LN\n+LM--YGKQFAN--GV---------------------------------F-\n+-E------NNQADFGANLMNQFSLSD---------NA--NLFLM-MVYRS\n+KG--S-K-DTAY-GY-KPQGMVTLMFSHSFL-N-KS-LEVYGGVMDAFNQ\n+----MGTY--D--RF---QN----PY-V-TND-K-H-FDNNI-RS-FRIG\n+LEYNFN--AT--QS---------K-------------YKGQQ-AD-GD-Q\n+---------K---NR-M---------------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n+>553178.CAPGI0001_2464\n+--------------------------------------------------\n+--------------------------------------------------\n+----------M--KNIIL-SL----------L------------------\n+--------------------------------------------------\n+-----------------------L---------I----------------\n+ISAT----------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------T---\n+A--AQTTFRGTLVNP---DQKPVSDANIILM--SL--P-D-ST-L-VK-G\n+VISNGHGSFEL-P--NPA--N--SKK--VLIK-----ITHLE-YQG-EV-\n+--FPP-----T--SS------------N-LGTIVLI--P--T------S-\n+-N-ELDAVVV--TARRR---PILEQKGTRISTNVAQSTLQK-LPTTDMLL\n+NFLPGVSTSYTG--GGFEVFGKGNPIFYINNRRVRNLD-------EVYQL\n+SPKDIERIEMETQPGAAFDNT-VGAVIYIILKK--------K---PGDGL\n+SGAAENTFY------F----F---KK-----------G------------\n+IMDETWLS--LNYRKGK-TD-WFTSISN-------DNH-F-NQ-ED--YN\n+VAQD--------LQVF----TQNN--------------------------\n+----------------Q--W----RVLNDETRQNQHKN-IKTKIGFAHE-\n+FSE-----EHSLGMSIRG-S-IIPF-I-GHNFST-QE-T--T-----T--\n+Y---------K--N--------QLLTARG----RN--EYDQF-EQ-----\n+-DK--KL-SVNAYYE-G-KLT-D-V--LK--MQTDVDYIGLRSDNTS---\n+-DIV--EHN--LLN-------------T-----------TS-------RN\n+------V--HTHSD----VISDWWGLKTTFF-QQL--G---K-------G\n+TLGYGVEVSNLHRTENYQD-------------------------------\n+--------------NV-LSAFNVKNTETRSDAFLSFSY-PI-K--KVNLK\n+LGTRYEYADFDYYE--NE---------------------Q-----K----\n+S------EA-K--------SKTY-RDWLPNVSVAFPW-E--K-TQITFSY\n+ARKIKRPAFHDLSDYNS-YVSSFLYNRGNPYITPQLTDEWNTLAT--YG-\n+------P----ISASVTYSHIHKGIYAD-YQ-L-S-S-------------\n+----------------------INSD----A---V-EK---------ILH\n+NYDDFSLL-KCALNAQ-KQ-I-G------------K-WMPK-------LT\n+LT--YEKPFAD--KV--------------------------------FY-\n+-K-------SEGLFSVEWMNQITPSE---------NW--LFLVM-LLYKS\n+KG--S-M-QEAY-IY-KPGSGVFVGVGRAFF-H-QS-LSVYAVASDFYNG\n+----L-NR-HA--RI---QN----SY-I-SNS-T-A-YSYSN-FS-FKIG\n+ISYNFN--TT--QS---------K-------------YKGKE-IS-EE-E\n+---------N---NR-M--------------'..b'--------------M-------------\n+--K-----I-L-I-------N--------L--------T--A-A------\n+--------------------------------------------------\n+-------------------L-L-L--G----S-GI--------V--L-A-\n+----Q----A----------------------------------------\n+--------------------------------------------------\n+---------------------------------------------PQP-L\n+TGK--GKVTGAVLD-E--KSQPFPFVNILLL--QA--K-D-SVL-V-K-G\n+IAADEDGKYAF-D--QVA--S--G-K--YLTL-----VSMVG-YQK-AY-\n+S-EPFN--V--K-D-T--------PV-N-LPTFTLK--T--D------T-\n+-Q-SLNEVTV--VAK-K---PFIEQEIDRTVVNVENSIVSA-GATALEVL\n+ERAPGVTVDQ-QN-EQLKLRGKEGVIVQIDGKQTFLSQ-Q-ELITLLRNT\n+PSDNIEKIELITNPSAKYDAAGNSGIINIKMKR--------N---KNYGT\n+NGNVNLGGA-----------W---A----------K-YG-----------\n+RA-NATGT--LNHRAGK-VS-SFISAGA-------FYN-K-GF-NN--N-\n+---D--I-Y--R---T----IPFED----KV-------------------\n+---------------TI--F----DQK--TERINRSEY-YNVRAGVDYF-\n+ATD-----KTTLGVLVSG-F-YN-D-W-SNP-FG-QT-N--T-----R--\n+I---------LN-E-----D-L-SLQRTF----RT--NVFNG-GK-----\n+-MN--NI-SSNLNLK-H-QFN-DKG--KE--LTFDLDYVHYGGKKKS---\n+-E-LD-TRY--FN-A------NG--TPDDA---------AT-------EI\n+------V--RND--MP--SDINIAMAKLDYT-QPI--G---K-------G\n+KFETGLKTSYVTSDNDMVFE--TF--I-D---------S-----------\n+--W-------Q-L-DP-KRSNRFKYTENVNAAYANYAG-AI-T-KKIKYQ\n+VGVRAEHTHSI-GN--S---------------------VT-----L----\n+N------QK-R--------DRNY-IDLFPSVFLSNQLDT--N-NVLNLSY\n+SRRIDRPNYQSLNPFEF-YLDPYTFQRGNPNLKPQYTHSFQLVHV--YK-\n+N-----A----LNTTLAYSRIKDMIADE--L-P-Q-Q-------------\n+------------------I---ASEN----K---T-FV---------TSD\n+NLDNQDNI-SLTVSFP-IP-V-T-----------KW-WQVQT-----NFT\n+GV--YNHYKSY--Y--L-----------------E-----------QQL-\n+-E------IKQVSWNMYASNQFTIG-----K--G--W--SAELS-GWYNS\n+RQ--F-Y-GLYA-A--RPMGMINAGVQKNIM-N-KK-GTIRLNVNDIFWT\n+----N-RF-NG--TA---VY----KD-I-DFR-V-R-SEWPS-RQ-FRLT\n+FTYNFG--NQ--NV---K-----G-------ARQR-N----T-GS-DD-L\n+---------Q---KR-AGG-N-----------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n+>761193.Runsl_4842\n+--------------------------------------------------\n+------------------------------------M-------------\n+--K-----T-F-T-------S--------L--------A--A-A------\n+--------------------------------------------------\n+-------------------F-L-L--L----T-AS--------L--S-A-\n+----Q----N----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+PGR--GKVSGEIKE-T--GGKPLPFATVLLL--KA--K-D-STL-V-K-G\n+AITSETGYYEV-E--NVV--E--G-R--YLIA-----ANMVG-FQK-TY-\n+S-TSFD--V--A-A-G-G------NV-Q-VPVLQVK--E--N------T-\n+-Q-TLQEVKV--IAK-K---PFVEQQIDRMVVNVENSIVSA-GGTALEVL\n+EKAPGVTIDR-QN-DRLQLKGRQGVMVMIDGKLQQISM-Q-DLMNMLQSM\n+PSDNVEKIELITNPPAKYDAAGNTGLINIVLKK--------N---KNFGT\n+NGNYTLSAG-----------V---G----------V-YE-----------\n+KL-NGSLG--LNHRNAK-IN-SFANVSV-------FHA-R-FQ-NT--Q-\n+---D--I-D--R---T----IAYKD----RI-------------------\n+---------------TY--L----DQN--SPRVGNPQN-LSFRAGVDYF-\n+VNK-----KTTVGVLASG-F-LN-Q-F-KMN--G-IS-S--T-----D--\n+F---------LD-R-----N-R-ILTGRF----AT--DAYNY-NR-----\n+-LD--NY-TGNLNLK-H-DFG--NG--RE--LTADADYSVFKGNSGN---\n+-D-LN-TTY--YD-P------KD--VVT-----------ST-------EI\n+------V--RNI--MP--STINIAAAKVDYI-HPL--K---N-------G\n+KLEAGAKSSIVNSDNDMRFE--TQ--V-D-------K-Q-----------\n+--W-------I-L-DP-SRSNRFKYKENINAVYTNYST-KL-D-KKTQLQ\n+LGLRAEHTHSE-GN--S---------------------VT-----L----\n+N------NV-V--------DRNY-VNLFPSVFVSRQLDT--N-NVLNVSY\n+SRRIDRPNYRNLNPFQF-FLDPLTFQQGNPNLRPQFTNSFQVTHV--FK-\n+G-----M----FSTTLGYSRINDVIADQ--I-P-K-Q-------------\n+------------------I---AEEN----K---T-YV---------TTE\n+NLDHQDNY-NVTFSIP-LT-V-R-----------KW-WTMQN-----NIS\n+AF--YNRYRSF--Y--Y-----------------G-----------ADL-\n+-D------LGQFGATVFVTNNFTLP-----K--G--Y--TAELG-GFWNS\n+PT--Q-Y-NILQ-A--RAQGQINVGIAKSLW-N-RK-ASLRLNVQDIFFQ\n+----N-RF-AG--TV---KY----RD-L-NFR-V-S-SRWES-RQ-VRLS\n+FTYRFG--NQ--NV---K-----A-------ARQR-G----T-ST-DD-L\n+---------R---NR-ANS-GQ----------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1071 @@\n+>445970.ALIPUT_00573\n+--------------------------------------------------\n+--------MKIILFSRQGV-VHTAG-DLHQMFDAIARF-GFDYAVNEEFA\n+PQIERLTGI-S-I---D-A--AHRYGRPM-G---PQ-PAESVLVCYGGDG\n+TLLDGIHRLGGAEIPVIGINSGHLGFLTSVPRNGCIGDVFELIAA-GKLE\n+CQPRSMLEVTGDFG---DGI-S--TRYAVNEVVIQR-QGAGMISVETYVN\n+DQMVATYHGDGLIVSTPTGSTAYSLSVGGPVVAPQCACLVLSPVAPHNLT\n+MRPVVIPSSSDVRLKVHARHAEISIATDNETCPIPE-G-AEFKVRLASRR\n+FFLAVPHNISFYDTLRKKMMWGVDIRS---------------------\n+>717959.AL1_21870\n+--------------------------------------------------\n+--------MKIILFSRAQI-AHTPE-EIRQLIGTIGAF-GFDYAVNEEFA\n+PLVEQATGT-A-L---P-P--ERIYGRYI-G---KQ-PAETVMVCYGGDG\n+TLLEGVHRLCGAPIPVMGINAGHLGFLTSAPSNGL-NLIFREIAE-GNIA\n+TEPRSMLRVTGEFA---RQP-E--SQLALNEFTVQR-HGAGMISVETYVD\n+RQMVATYHGDGVIVSTPTGSTAYSLSAGGPVVAPTCQCLVISPLAPHNLT\n+MRPVVIPDTGVITLNVDARRADAFVTLDNRTYPVSH-G-ASFTVERAEQT\n+IFLAVPHNISFYDTLRNKMMWGIDIRS---------------------\n+>908612.HMPREF9720_1546\n+--------------------------------------------------\n+--------MKIILFSRRQL-PHTAG-EICQLFEAFRIF-GFDYAVNEEFA\n+PLAEELTGI-R-I---P-P--EKIYGQCT-G---KQ-PANSVMVCYGGDG\n+TLLEGVHRLCGAPIPVMGINAGHLGFLTSAPSAGL-NLIFKEIAE-GRLT\n+TEARSMIEVTGDYA---EQP-D--TTLALNEFTVQR-HGAGMISVETYVD\n+DQMVATYHGDGVIFSTPTGSTAYSLSAGGPVVAPTCACLVISPLAPHNLT\n+MRPVVIPDTAVITLHVHTRRSDAFVTLDNRVYAVGQ-E-ATFTVKRAEQK\n+IFLAVPHNISFYDTLRNKMMWGIDIRS---------------------\n+>709991.Odosp_2154\n+--------------------------------------------------\n+--------MTVAIYGRSIE-PEFFP-YLKRLVEGLERK-GVGMVCEEKFA\n+ALLSGNYGYEP-K-----F--LNCFGRCT-L---IK-EEVELLLSVGGDG\n+TFLDSVIYVKDSGVPVLGVNSGHLGFLANVPVEEI-EDAVDFIAA-GKYE\n+VEQRDMLQLEVEGQ-R--IA-D--FDYALNEVGVLKAATSSLLKIHAYIG\n+ENYLTTYWADGLVVATPTGSTAYSLSGGGPIVSPECRNIILTPICPHNLT\n+IRPLVVPNTAEVRLKVEGRSGEYVLCMDSRIRKMTD-G-QELKICTGSQK\n+INVVKLPRHNYYDTLRNKLMWGEDRRNGMKD-----------------\n+>879243.Poras_0689\n+--------------------------------------------------\n+-------------------M-RLTD-DVTALLTALAEH-GVDLYIEAPLW\n+EALQLAGIP---------EGYPQ---MRLGG---ET-PYGDIALSLGGDG\n+TLLRAVHKLRDVELPIWAINCGHLGFMTEMEPQEA-LHHLDDLLA-GQYD\n+IETRSLIDVSVAG------E-H--VGTALNDLAVQKRETGSIIKIRVDLD\n+GNLLAEYAADGLVVSTPSGSTAYALSLGGPIVTPQCQTLLLVPIAPHTLN\n+MAPLIFPDTSVLTMRVSSLHPTFSIVIDGNLRVYDC-G-VEIVARKSDKR\n+AHLLRLSHKPYAQVIREKLLWGRDLR----------------------\n+>596327.PORUE0001_1563\n+--------------------MVG----SFGVSLLF------GTFVAMQAD\n+SQMDRHKINTIAVYGSHDTL-RLTD-DVAALLTALAEH-GVDLYIETPLW\n+EALSQAGIP---------EGYPQ---MRLGG---ET-PYGDIALSLGGDG\n+TLLRAVHKLRDVELPIWAINCGHLGFMTEMEPQEA-WHHLDDLLA-GQYS\n+IETRTLIDVSVAG------E-H--VGTALNDLAVQKRETGSIIKIRADLD\n+GDLLAEYAADGLVVSTPSGSTAYALSLGGPIVTPQCQTLLLVPIAPHTLN\n+MAPLIFPDTSVLTMRVSSLHPTFSIVIDGNLRVYDC-G-VEIVARKSDKR\n+AHLLRLSHKPYTQVIREKLLWGRDLR----------------------\n+>518766.Rmar_1525\n+--------------------------------------------------\n+--------MIYGITGNTQKE-QLWK-PVGELIRWMARQ-GLEVRLHPDVA\n+RGLVARGLLSD-----D-EAAAL---TAH-D---LA-AEVDLLLSFGGDG\n+TLLQSAHLAGRRGTPVLGVNIGRMGFLADVEVEQV-REAIRTIEA-GDYH\n+LEARMVLEAELEDG-P--VP-E--LPWALNEFVIDRSGLAGLITIDVTVD\n+GVSLTRYWADGLIFSTPTGSTAYSLSAGGPIVSPECEVVILTPIAPHTLT\n+LRPIVLPASVEIEARVYTGGQPYVLAADGRSQLIHR-EGQRITIRRAEHT\n+VNLVKLPGQHYFQTLRSKLMWGVR------------------------\n+>309807.SRU_1609\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------MCRAH---AVD-D---VA-AAGDIVLSFGGDG\n+TLLRTAHRTGPNGTPLLGVNIGRLGFLADIEIGQI-HDAIDALEA-GNYR\n+TEERLALQADLESD-S--GL-D--TEWALNEFVLDRSGAAGLIEIEVAVD\n+GTPLNTYWADGLIISTPTGSTAYSLSTGGPIITPGVDAIILTPIAPHTLT\n+VRPIVLPADATITCQVRENDQPYVFAADGQSTMFDE-HNLEFSVERANHA\n+VNLVKLPGQHFFHTLRSKLMWGARRSEGPTDRGQSISAPRDQSPLKGE\n+>575590.HMPREF0156_01661\n+--------------------------------------------------\n+--------MRIAIFGTTYDH-HYNQ-CLQDVVNILGSN-GASIIFEKTFR\n+KYIDGQITLSG-----V-ETA------EA-D----S-VDADIAISFGGDG\n+TFLATSQMLAKKGTPILGINAGHLGFLADVSAHEL-EQVLLDILS-GRYK\n+IEKRVMLQMKLSND-T---N-T--SYTALNEIAILRHDTSSMIAVDVTID\n+GEFVANYKSDGLLVATPTGSTAYSLSLGGPIVSPNSANFLIVPIAPHSLT\n+VRPLVIRDDCRIDVCVKSRSGNYRIGVDGHSINLDE-S-TTIAIEKSRYQ\n+TNSIQPLDHTFFRTLSNKLMWGADTRV---------------------\n+>694427.Palpr_2865\n+----------------------------------------'..b'QHLISLDSRIATLDN-E-TIITLEKAPFE\n+ISLIRLEGDSFLKTLRRKLLWGEDKRN---------------------\n+>487797.Flav3CDRAFT_0698\n+--------------------------------------------------\n+-----MVQLNVALFGYLPS-EITVK-ALVGILEAIEAV-GGKASIENNFK\n+EAIASFNET-SLHALLS-P--LGTFSSQE-E---VP-KETSLFVSFGGDG\n+TMLKAITYIKDSGIPLVGVNTGRLGFLSTIDVGAV-QKVITDFVA-GAYT\n+IEERSMVGLYTNHP-IDAFR-E--VNVALNEITVSRKDTTAMITVATYLD\n+GEYLTSYWADGLIIATPTGSTGYSLSCGGPVMAPGTNSLILTPIAPHNLN\n+ARPLIITDHTEIRLVVSGREQQHLVSLDSRIASIDN-G-TELVIKKAPYT\n+LKMVAYTSESFLKTLRKKLLWGEDKRN---------------------\n+>313596.RB2501_03280\n+--------------------------------------------------\n+--------MKVALYGQTYN-DDASG-PVREILDELDDG-ESTVALESEFC\n+RYLGLDS---------R-G--YDTFDQNG-G---LD-GSFDLFISFGGDG\n+TILRAITYIRESAIPIVGVNTGRLGFLSTFRKEEV-RSLLEEFRA-GAYR\n+IVERSLVEASLEGD-TPGGG-Q--LNFALNEVTVSRKDTTSMITVETYLD\n+GEYLTSYWADGLIVATPTGSTGYSLSCGGPVIAPTAKSLVITPIAPHNLN\n+ARPLVIDDDTVIRLRVSGREQQHLLSLDSRITSVDN-G-TEITVRRAPFT\n+IRMVEYTSESFFKTIRKKLLWGEDRRN---------------------\n+>886377.Murru_1923\n+--------------------------------------------------\n+--------MKVAIYGQSFQ-QEDQL-CVVELLDELKKL-DASVYVEENFN\n+KLVATITK--E-----Q-V--KGTFTQSK-G---LD-SSFDMFVSFGGDG\n+TMLRAVTYIKDYGIPIVGVNTGRLGFLSTFKKENV-RKLVTEFET-GHYT\n+IEERSLVEVELNSE-LDEFN-G--LNFALNEITVSRKDTTSMITVETWLD\n+DEYLTSYWSDGLIVSTPTGSTGYSLSCGGPVIAPSAESLVLTPIAPHNLN\n+ARPLVISDKTQIRLKVSGREQTHLVSLDSRIADIPN-G-KEIRIKKADFT\n+IKMIEYKSESFLKTLRNKLLWGEDRRN---------------------\n+>867900.Celly_1943\n+--------------------------------------------------\n+--------MKVAIYGQTYN-DDTVD-YVCELLSELKLH-NANISFEKDFY\n+NFVTASKE--I-----E-D--FSIFTENS-G---LD-ASFDMFVSFGGDG\n+TILRAITFVKDLGIPIVGVNTGRLGFLSTFKKEDV-KKVVQEFVA-KDYT\n+IVDRSLVAVTSNVN-IPEFN-A--INFALNEVTVSRKDTTSMITVETSLN\n+NEYLNSYWADGLIVSTPTGSTGYSLSCGGPVITPTAKSLVITPIAPHNLN\n+ARPLVISDNTVVKLKVSGREKNHLLSLDSRIVTLEN-G-TEITVKKADFT\n+VKLIEYTSESFLKTLRNKLLWGEDKRN---------------------\n+>688270.Celal_2133\n+--------------------------------------------------\n+--------MKVAIYGQTYS-DNALD-YVVELLDELRTI-PAEVYFEEDFY\n+QLLKSSRT--V-----E-E--FNVFTAES-G---LD-DSFNMFVSFGGDG\n+TILRAITYVRDLNIPIVGVNTGRLGFLSTFKKEDV-RKVVKEFIS-GAYT\n+IVERSLVEVYTDPQ-LPEFE-N--LNFALNEVTVSRKDTTSMITVETHLN\n+NEYLTSYWADGLIVATPTGSTGYSLSCGGPVIAPSAKSLILTPIAPHNLN\n+ARPLVISDDTEIRLKVSGREENHLVSLDSRIATVEN-G-REIIIKKSSIT\n+IKMIEYTSESFLKTLRNKLLWGEDKRN---------------------\n+>313603.FB2170_02740\n+--------------------------------------------------\n+--------MKVAIYGQTYQ-DNTFD-YVLELLDELEKE-SATIFIEENLN\n+THLSHKHS--S-----S-S--YETFNELI-G---LD-DSFDMFISFGGDG\n+TILRATTYVRDLNIPIVGVNTGRLGFLSTFKKEDV-RKVVQEFVE-GAYT\n+IVERSLVELNAGPQ-AEEFG-E--LNFALNEITVSRKDTTSMITVETHLN\n+GEYLTSYWADGLIVSTPTGSTGYSLSCGGPVIVPTAKSLVLTPIAPHNLN\n+ARPLVISDDTVIRLKVSGREDNHLVSLDSRIATLEN-G-KEIEIKKADFT\n+IKMIEYNSESFLKTLRNKLLWGEDKRN---------------------\n+>391603.FBALC1_14952\n+--------------------------------------------------\n+--------MKIAVYGQNYIKGTTQK-AVEKLLNFLLEK-EANVFFEQEFI\n+KTQNTAI---------Q-N--NSAVRVFD-K---LN-DTFDLLISVGGDG\n+TILRAITYVRDLGIPIVGINTGRLGFLATIQTDEI-ESALSEIFK-GDYK\n+ISKRSLLSVSTEPK-NKDII-E--THFALNEIALSRKNTTSMITVETHLN\n+DEYLTSYWADGLILSTPTGSTGYSLSCGGPVITPDANNFALTPIAPHNLS\n+ARPLIIPDNTIVTFRVNGREDQFLMSLDSRIVTLPN-T-TTVTVKKADFA\n+IKMVELLDETFLDTLRKKLLWGEDRRN---------------------\n+>983544.Lacal_1413\n+--------------------------------------------------\n+--------MKVAIYSQYPK-KQSKD-SLEILTTELLKL-EATLFLEIEFF\n+NNIKNKLL----------N--PDAYKTFN-K---LD-KSFDLFVSIGGDG\n+TILRAVTYIKDLNIPVIGINTGRLGFLATIQPENI-KEAIQQIKN-KAYT\n+LSKRTLLSIETTPE-NNEIK-N--VNFALNEIAISRKNTTSMITVDTKLN\n+GEFLTSYWSDGLIISTPTGSTGYSLSCAGPVITPDTTSFVLTPIAPHNLS\n+ARPLVIEDSTVIELKVSGREDNYLVSLDSRIATLSN-D-TIITIKKSPFT\n+INMIELNTESFLTTLRKKLLWGEDKRN---------------------\n+>1046627.BZARG_1974\n+--------------------------------------------------\n+--------MKIAIFGQAFN-SNTEE-ALVVILHYLNNREGVSVFLIAEFN\n+EKIQEKKP--------S-E--FNFTKITD-T---LD-PSFDLLISIGGDG\n+TILRAVTYVHDLNIPVIGVNTGRLGFLATIQNQLI-IPSLDAIFN-KAYR\n+ISERHLLVIDTFPK-VSAFD-T--YNFALNEIAVSRKNTTSMISVETRLN\n+DEYLTSYWSDGLIVSTPTGSTGYSLSCGGPVITPDTNSLVITPISPHNLS\n+ARPLVVKDSTEVKLKVNGREDNFLVSLDSRITTLSN-E-TIITIKKAPFT\n+IKMIELLEESFLDTLRKKLLWGEDKRN---------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,11900 @@\n+>504472.Slin_5005\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------M--NK---S--TMHR-L----L-----\n+------VL--A------------------------------------GIA\n+I----S--------------------------------------------\n+---------LV----------------------------S------I---\n+--------------------------------------------------\n+----------------------------------------QVAEA---QK\n+QPVDLVNPLVDAANSR---------W--------------------FFFN\n+SASRPFGMVNLSPDNGI------N--------------ADWGAGYRYHQD\n+SIKCFSHIH----G--WQLSGVPVMPTTGE-FKGHLGAEQY---------\n+--------------------------GSRFSHQKEIVKAGYHKVVLDAYN\n+IIAELTSTTRVGFHKYTYPA--SA----QSHILFDFSTFLGP---S----\n+--DTQKGYVKKV--------SN-------QE--IEGYAIMAPT----I--\n+---RRPKVLPVYFVAVFDKPFDSFRGWRNGKLE-----------------\n+------------------------T------------------I---SG-\n+---V-----IEGERVGAYLSFK--T-KA-GEVRKMKVAISYVSEEQARIN\n+LKTELS----------HWDFEKTVQDSRSDWNNWLSRIDVQGGSDT----\n+-------------------------------TRSRFYTDLWHALQGRRII\n+SDVNGKYSDMTGPERRIKQIPLD-----ANGK-PKFNHHNSDSFWGAQWT\n+INTLWHLV-YPEVTESFVNSMVMMYQDG--GLIPRGPAGGNYTYVMTGAS\n+TTPFIVSAYLKGI-RGFDTEKAYEGLRKNHFPG-GMMS------------\n+----K---AGYEH-NTF-KGGGIEYYM--ERGYVPHP-----LSKTRYGF\n+HQDGSTQTLEYAYQDYTLAQMAKSLGKT-DDYNLFMKRAQNYKN-VWNPD\n+LGWMWNRTLD-GK-WAEP-V-------------------DILRYD-----\n+----NGWEEGNAAQYTWFVP-HDVQGLITLMGGREKFTAKLNSSFEKAQK\n+H-DY-VSGKSHDNETLEELRRVFLNYGNQPSIQTAHLFNYA-GAPWLTQY\n+WTRQVIEKVYSGLSPDY--GYSGDEDQGLMGSLSVLLKTGLFSTNGGTTP\n+EPFYEI-SSPIFDRITIKLNPKYYKGKQFVIDAKNNS--AANLYIQSAQL\n+NGKPL--DRPWMLHETVVNGGTLTLQMGAQPNKSWGNKPE-QAPVSMSSE\n+AAKR----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------\n+>880070.Cycma_2925\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------M--LK---L--LV--------------\n+-------N--L-------------------------L--------T--FV\n+LV---I--------------------------------------------\n+---------PS----------------------------M------G---\n+--------------------------------------------------\n+----------------------------------------FQLNP---DP\n+KPIDKVYPLLDAANSR---------W--------------------FYFS\n+AATRPFGMVNLSPDHEI------D------G------AW--GSGYRYNSD\n+TVKGFSHIH----A--WQMSGVSVMPVSYD---TA--P-EVL-----L--\n+-----------------------TDYYSTYDRDLETIKPGYHKVFLKRYG\n+ITAELTATHRVGLHKYTFPE--AR----NQAVLFHLEGILGP---S----\n+--KMIDGSLKQI--------SP-------YI--LEGQVTNSPT----S--\n+---RRPNTLTVYFQVEFDQPIVD---WVASENS-----------------\n+------------------------P-------------------------\n+---------------HKIVSFG--K-SK-GKPLQMKVALSYTTAENAALN\n+KKEELP----------HWNFDKVVKETQEIWNELLGRIEVEGNTET----\n+---------------------'..b'--------G--K--KGYRAHFSHDNESAEPGYYKVHLDSTN\n+IDVELTVSLRSGLHKYQFPS--SD----NQFVILDLVHR------D----\n+--KVLDAKIDKI--------SD-------T-E-IVGYR----HS-EAW--\n+---A--KDQRLFYAIKTSHPFKDMLQ--SP--------------------\n+-------------------------------------------P---QT-\n+---GM-PG-----ARRSSLKFI-N--PN-NEPIIIKVGISAVDIEGAKQN\n+MQAEIG----------NKDFETVKKEAQTYWESQLEKVVIESNDLD----\n+-------------------------------KKTNFYSALYHTMLAPQRY\n+QDVDGRYRG------------MDLKI--HNAD---FDYYSVFSLWDTYRA\n+AHPLYTIIE-QERTNDFINTFLAKYDEG--GIMPMWDLAGNYTDCMIGYH\n+AVPVIADAYLKGI-RGYDTDKAFEAMKHSATRD-K---------------\n+--------------------FGLEAYK--KYGFIPVD-----E-------\n+ESESVSKTLEYAYDDWTIAQMAKDMGKT-EDYETYIKRAQYYKN-VFDPE\n+TQFMRGRF-RN-T-WFAP-F-------------------DPYEVN-----\n+----FNYTEANSWQYSFYVP-QDVSGFIELLGGKGKLEVQLDELFSAKTE\n+T----SGRDQSD----ITGLIGQYAHGNEPSHHMAYLYNFV-NKPHKTQE\n+KVHQILTELYNND-P-D--GVSGNEDCGQMSAWYVLSSMGFYSVTPGSNQ\n+---YVI-GTPLFDKATINLES----GKQFTIVANNLS-D-TNKYVEYVKL\n+NGKDL--DVTYLNHEDIIAGGTLEFTMTDNSAV-WGSRAG-NEPTTEIKD\n+HIILPSPFIAKG-DITFRGSTEVVLATSEK----EAKIYYAIDNE-----\n+---AYKLYKKPFSITEDT----------KLKLYSE-KG-DL---------\n+KSPVLTTPFYKIDPNLRITLESKFANQYSAGGNDALIDGIRSTKNYRTGS\n+WQGYNDSDVIATVDLGSQKNIS-SVKVNFLQ-------------------\n+--------------------------------------------------\n+DQGAWIFYPTEVQCFVS--KD-NITFK-A-LTSQKINASKRDSELK----\n+-IKTI------DFKIPNI--------------------------------\n+-----SYKYVKIIAKKLGKVPE--WH-----VGYPYDGRSWIFVDEISI-\n+K-------------------------------------------------\n+----------------\n+>391587.KAOT1_08253\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------M--KLQH------IT----------------------L-----\n+-------FI------------------------------------VI---\n+----SL-F------------------------------------------\n+--------FSCS-------------N--D---------E------KI---\n+--------------------------------------------------\n+---------------------------------------Q-IAQK---DT\n+DLIDYVNPFIGT-------GG-------------H----------GHTYP\n+GATMPFGMMQLSPDTRL------D------------G-WDGCSGYHYSDE\n+YIYGFSHTH-LSGTGVSDYGDILLMP-TNE-I----------N-F-NNGS\n+D--------TSAN--SAT--K--KGYRAHFSHDNEVAEAGYYKVLLDSTN\n+IEVELTVSERSGIHKYSFPS--AE----NQVVMLDLVHR------D----\n+--KVLDAKIEKV--------SD-------T-E-IVGYR----FS-EAW--\n+---A--SDQRLFYVLKTSHPFEDMLQ--SP--------------------\n+-------------------------------------------P---KT-\n+---GM-PG-----GRRSALTFK-N--PN-NEPIIIKVGISAVDIEGARKN\n+LEQEIG----------TKSFEEVKKIAQETWEKQLEKIVIESEDVD----\n+-------------------------------YKTNFYTALYHTMIAPNIY\n+QDVDGRYRD------------MDMKI--HQSD-D-HTHYTVFSLWDTYRA\n+AHPLYTIIE-QERTNDFIKTFIKKYESG--GIMPIWDLSANYTGCMIGYH\n+AVPVISDAYMKGI-RDYDVEKAFEAMKHSATRD-K---------------\n+--------------------LGLKYYK--TLGYIPVE-----M-------\n+ESESVSKTLEYAYDDWTIAEMAKAMGKT-ADYEEFIKRAQYYKN-IYDPE\n+TKFMRGRF-RN-T-WFSP-F-------------------DPYEVN-----\n+----FNYTEANSWQYSFYVP-QDVSGFIDLLGGKDKLEAQLDKLFTANQE\n+T----SGRNQAD----ITGLIGQYAHGNEPSHHMAYLYNFI-NKPSKTQE\n+YVHQILTTLYKNE-P-D--GVSGNEDCGQMSAWYVLSSLGFYSVTPGTNE\n+---YII-GTPLFDKATINLEN----GKTFTIIANNSS-K-ENIYIKSAML\n+NGKNH--PKTYLNHADIMNGGTLVFEMTNTPTD-WGTKDE-HIPVTEIKE\n+HKIVPPPFIAKG-DIAFKGSTEVVLETVDK----KSTIYYRMMNVYQS--\n+FKPDFVVYDKPIKIENKS----------FLEVYAQ-RG-EE---------\n+KSAIITTDFFKIDPNLKIKLETEYANQYNAGGQNALIDGIFGTEDFRTGT\n+WQGYFDTDVIATVDLGKVKPIH-TIQVNFLE-------------------\n+--------------------------------------------------\n+DQKSWIFLPTEVECYVS--DN-PNRFYKS-LPTQTFEVTKPKEGAH----\n+-IKNV------SFDMKGY--------------------------------\n+-----SGRYVKIVAKKLGELPE--WH-----LGYKHNGRSWLFVDEIEV-\n+K-------------------------------------------------\n+----------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,2985 @@\n+>709991.Odosp_0661\n+--------------------------------------------------\n+-------------------------------------------------M\n+------------------------------------------------RT\n+IAILCGGGPAPGINTVVATVTKVFLKDGFR-------VLAIHEGYKGLFA\n+AHPEVEELTYEKADQIYSRGGSAIKMSRFKP----EDQDFTTALFVKEGI\n+ELLVTIGGDDTASTANRLTKYLAAHQV-NIRNIHVPKTIDNDLPLPEGIP\n+TFGFTSAKEMGVTIGKV--IKAEASTTQNWYLLMSMGREAGHLAFEIGKG\n+IHASMIIIPEMFNKTQITIDKIVRLIISSMIKRRIVGQKFGVV-VVGEGI\n+FHFLQDEDIASSGITFDYDAHGHPELSEVSK-------------------\n+------------------AHVISKILKNR---LKELNLDIICRPVE----\n+--------------------------VGYSLRCVDPSAFDLTYCTTLGIG\n+VKKLYDEGHSGCMVAVNLEEEVI--------PVYLKDVED-EHGKIRTRL\n+VNIDKEVVR----QTLAENIYYLTAQDRSLARKWLADPEPFEY----ERI\n+LG---------------\n+>688270.Celal_4209\n+--------------------------------------------------\n+-----------------------------------------------MAS\n+------------------------------------------------KS\n+ILIICGGGPAPGINAVISTVAKIFLKDGYR-------VLGLHEGFKGIFS\n+ENPEIKEFDFAHADRIFSRGGSTLIMSRFKP----SDEKINTELFAQNNV\n+KLLVSIGGDDTASTANRITTYLSKENI-SIANIHVPKTIDNDLPLPDRNP\n+TFGFHSAKDEGVRIGNT--TYEDARTSQNWFVMSTMGRSAGHLAFGIAAS\n+CHFPMMVIPEMFNKTEVTFDKVVRLIISSIIKRKIENINYGVA-LISEGI\n+FHIMPDSELQNCGINFTYDDHGHPELGNVSK-------------------\n+------------------SHIFNMLVQRK---LKELGVNIKSRPVE----\n+--------------------------LGYELRCCRPIGFDLTLCTLLGLG\n+VKKLYDEGISGCIVTANSKGEIS--------PLYLKDLQD-KEGKIAPRL\n+VDINSEFAK----LCFQN-LHYLTESDFDKAKQYLDNPKDYYF----NDI\n+LEDAY------------\n+>445970.ALIPUT_01805\n+--------------------------------------------------\n+---------------------------------------MLS-----M-S\n+YKI-----------------RY------------------DMTKRN--EA\n+IAILTGGGPAPGMNTVVGSVAKTFLQKGYS-------VIGLHKGFTGLFR\n+EAPATENITFLKADEIFNLAGSFLRMSRFKPSDEDFEKRFNWQFFTENNI\n+KLLVTIGGDDTASTANRVAKFLEEKRH-PIANIHVPKTIDNDLPLPDCAP\n+TFGYESAKDKGAVIARA-VYVDARTSGN-WFVMSAMGRSAGHLAFGIGEA\n+CHYPMIVIPEMFNKTPITIDKIIRLMVSSIVKRRIVGMDYGAA-VISEGV\n+FHELSEAELSSCGIHFTYDAHGHPELGKVSK-------------------\n+------------------ACFFSMLLDQR---LAELKLNVQTRPVE----\n+--------------------------LGYEIRGQTPVAYDLTYCSELGIG\n+VYKLFSEGKTGCMVYVDGCGNVE--------PLYLKDLQDPATGKILPRM\n+VDISSDRFK----AVVDNILMAITPPDYEAARQYLSNPEEYDF----CKI\n+LGWDETDL---------\n+>717959.AL1_03080\n+--------------------------------------------------\n+--------------------------------------------------\n+-MK-----------------EA----------------------------\n+IAILTGGGPAPGMNTVVGSVAKTFLRQGYR-------VIGLHEGYTGLFN\n+PSPRTVDIDYPMADGIFNQGGSFLQMSRFKPKDSDFENNFNLKFFTDNNI\n+KLLVTVGGDDTASTANRIAKFLEAKKY-PIANIHVPKTIDNDLPLPKGTP\n+TFGYESAKDKGAVIARA-VYVDARTSGN-WFVLAAMGRSAGHLAFGIGEA\n+CHYPMIVIPEMFDKTEITVEKIVNLVISSIIKRKIMGMDYGAA-VISEGV\n+FHALSDEEIRKSGIHFTYDEHGHPELGKVSK-------------------\n+------------------AHIFNEMIEMK---LKELGLKVKSRPVE----\n+--------------------------LGYEIRCQTPIAYDLTYCSELGIG\n+VHKLFAEGKTGCMVYVDSEGNVS--------PLYLKDLQDPTTGKIPPRL\n+VDIKSDKFT----SVVETILNAITPADYEAAKAYVPNPEEYDF----HKI\n+LNWK-------------\n+>908612.HMPREF9720_1126\n+--------------------------------------------------\n+--------------------------------------------------\n+-MK-----------------EA----------------------------\n+IAILTGGGPAPGMNTVVGSVAKTFLRKGYR-------VIGLHEGYTGLFN\n+PSPRTVDIDYPMADGIFNQGGSFLQMSRFKPKDSDFENNFNLKFFTDNNI\n+KLLVTVGGDDTASTANRIAKFLEAKKY-PIANIHVPKTIDNDLPLPKGTP\n+TFGYESAKDKGAVIARA-VYVDARTSGN-WFVLAAMGRSAGHLAFGIGEA\n+CHYPMIVIPEMFDKTEITVEKIVNLVISSIIKRKIMGMDYGAA-VISEGV\n+FHALSDEEIRKSGIHFTYDEHGHPELGKVSK-------------------\n+------------------AHIFNEMIEKK---VKELGIKVKSRPVE----\n+--------------------------LGYEIRCQTPIAYDLTYCSELGIG\n+VHKLFAEGKTGCMVYVDSEGNVS--------PLYLKDLQDPTTGKIPPRL\n+VDIKSDKFS----SVVETILNAITPADYEAAKQYVPNPEEYDF----HKI\n+LNWK-------------\n+>553175.POREN0001_0958\n+--------------------------------------------------\n+----------------------MTYIRLDKLRAIYKPQLPEVLE------\n+--HPTKLDVSTNAATPDERIAALFPHTAQLPVVSLAEA-GAEAEATSPLT\n+VGVLLSGGQAPGGHNVI-----AGIFDALKMHHPASILYGFIMGPGGLLR\n+GE--ARELTADVINCYRNTGGFDMIGSDRTKLETKEQFEQVLLHAHRLAL\n+DALVVIGGDDSNTNAALLAEYCRSVND-PLCVVGCPKTIDGDLKNGWVET\n+SFGFDTCVKVYAELVGNIQ-RDCYSSKKYWHFVKLMGRSASHLTLECALM\n+TQPTVAIISE'..b'GAVVFNE-----EH-DFPIVGMPGTIDNDINGT--DH\n+TIGYDTALNTVVEAIDK-I-RDTANSHNRLFLVEVMGRDAGDIALNAGIG\n+AGAEEILIPEE--------DLGTDRLLESLKRSKKSGKTSSII-VVSEGD\n+-----KI--GK----------NIFELAEFIE-------------------\n+---------------------------TN---LEDYEVRVTV--------\n+--------------------------LGHIQRGGTPSCYDRVLASRLGIG\n+AVDALLAGERDIMIGTVHGKVTS-------VPFKEAVAGR-N--KIDLDL\n+IRVADITST-----------------------------------------\n+-----------------\n+>706194.SMCARI_278\n+--------------------------------------------------\n+-----------------------------------------------M--\n+-NI-----------------GK----------------------------\n+IGILTSGGDSPGMNAAIRAVVRTASYYCVN-------CIGISLGYKGLIN\n+NE--MRKVVPTDVNNLIHRGGTILKTARSEEFKTKFGRKKANINYKKNGL\n+EGLIVIGGDGSFTGAMIFGQ-----EY-NIPIIGIPGTIDNDIYGT--DF\n+TVGYDTALNTAIEAIDK-I-RDTATSHNRLFFIEVMGKDSGFIALNSGIA\n+TGALDILIPEK--------KYNLDKLFYSIEKVKQKGKYSSII-IVSEGK\n+-----KL--G-----------GVYDLAKTTK-------------------\n+---------------------------KK---FPDYDIRVSI--------\n+--------------------------LGHIQRGGYPTCSDRVLASRLGVA\n+SVEALISGKKNVMTGIKANKVIF-------TPFLKAIKKK-R--KIDIDL\n+IKISDIIAC-----------------------------------------\n+-----------------\n+>865938.Weevi_1531\n+--------------------------------------------------\n+--------------------------------------------------\n+--M-----------------KR----------------------------\n+VGVLTSGGDSPGMNAAIRAVVRSCRYYNLE-------SVGILQGYEGLIQ\n+ND--MLTLGPRSVKNIINQGGTILKTARSEEFRTIEGRKKAYQNIQKNNI\n+DGLIVIGGDGSFKGANIFHQ-----EF-NLPFIGIPGTIDNDIFGT--DY\n+TIGYDTALNTVVEAVDK-L-RDTATSHDRVFFVEVMGRDAGFIALNSGIA\n+SGAQNILIPEK--------KDHINELIQSLEQSAKSGKKSSIV-VVAEGE\n+-----EL--G-----------NVYELAKQVK-------------------\n+---------------------------AK---HPDYDIRVTV--------\n+--------------------------LGHIQRGGNPSCQDRVLASRLGIA\n+AVEALMKGKTNVMTGLRSNKIVY-------TPIEEAIQKH-H--SIDNEL\n+LKVAKILAI-----------------------------------------\n+-----------------\n+>992406.RIA_1658\n+--------------------------------------------------\n+-------------------------------------------MSE-S--\n+-KL-----------------KR----------------------------\n+IGVLTSGGDSPGMNAAIRAVVRTAHYYGIE-------CMGIREGYNGLIE\n+GN--MIKMGPRSVKNIINQGGTILKSARSKEFRTVEGRLKAFEQCQKNEI\n+GALVCIGGDGTFTGAKVFSE-----EY-GIKVVGVPGTIDNDIFGT--DF\n+TIGYDTALNTAVEAIDK-I-RDTATSHNRVFFVEVMGRDAGFIALNSGIA\n+SGAIDILIPER--------KDSLEEMFENFHNAQKRGKTSSIV-VVAEGE\n+-----QL--A-----------STYELAEKTQ-------------------\n+---------------------------KE---FPDYDIRVAI--------\n+--------------------------LGHIQRGGMPSCADRVLASRLGYG\n+AVEGLRKGLTNVMAGIRANQLVF-------TPIEDAIKKH-N--EINQDL\n+LKISEILAM-----------------------------------------\n+-----------------\n+>531844.FIC_00682\n+--------------------------------------------------\n+-------------------------------------------MKE-S--\n+-AV-----------------KK----------------------------\n+IAVFTSGGDAPGMNAALRAVVRTANHYNIE-------CYGVREGYNGLIH\n+DD--FTRMGPRSVKNIITEGGTVLKSARSEEFKTKAGRQKAYDNCVKHGI\n+DALVCIGGDGTFRGANIFNE-----EF-GIKVIGVPGTIDNDIFGT--DN\n+TIGYDTALNTAMEAIDK-I-RDTATSHNRVFFVEVMGRDAGFIALNSGLA\n+TGAIDILIPEK--------KDSIDDLFKTFERAEKAGKSSSIV-VVAEGE\n+-----KL--G-----------SIYDLAKATK-------------------\n+---------------------------AG---FPDYDIRVAV--------\n+--------------------------LGHIQRGGSPSCADRVLASQLGYG\n+AVVGLMEGRTNVMAGLKSNVLVY-------TPIEEAIKKH-N--EIDAGL\n+LKISEILAI-----------------------------------------\n+-----------------\n+>525257.HMPREF0204_11870\n+--------------------------------------------------\n+-------------------------------------------MKE-S--\n+-VV-----------------KK----------------------------\n+IAVLTSGGDSPGMNAALRAVVRTANYYNIE-------CYGVREGYNGLIN\n+ND--FLKMGARSVKNIINQGGTILKSARSAEFRTKEGRQKAYDNCVKLGI\n+DGLVCIGGDGTFTGAKIFNE-----EF-GIRVIGIPGTIDNDIFGT--DN\n+TIGYDTALNTAMDAIDK-I-RDTATSHNRVFFVEVMGRDAGFIALNSGLA\n+TGALDILIPEK--------KDSIDELFAKFRDAEKTGKASSIV-VVAEGE\n+-----KL--A-----------NVYELAEKTK-------------------\n+---------------------------QT---FPDYDIRVAI--------\n+--------------------------LGHMQRGGSPSCADRVLASRLGYG\n+AVTGLMEGQTNVMAGMRSNDLTY-------TPIEEAIKKH-N--EINKDL\n+LLISKILAI-----------------------------------------\n+-----------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,3978 @@\n+>926562.Oweho_3187\n+--------------------------------------------------\n+----------------------------------------------MQKI\n+KYFIR--PR-YD-I----------NADGF--TLVELNLR-------IDGL\n+E--TRI-SLEYYLQLKYWDRKKRVMVAK------KGLTKTEA-L------\n+----------QINLELQGYIDRCAEIVRNARMNGEFLSLQSFESKLWYTG\n+K-------------------------PLNLIEFTENWIEENP----D---\n+---N--NASSSLKTYSKLIGVWKDAFGNTVGLGDIPDIRPKIE-------\n+--KAMLKRKHSL----------------------------NTRKKNHSKT\n+KSMIKRAIK-AGYPITNPY--TEP-IGGIKG-N-RNFLNPDELRLAIKIY\n+KRDYL-PDH-LQKTLKVFLFACFTGCRISDMQELRKNNI---VGDSLQYI\n+AVKTR------RYQ-KRVEVPLP-EVARALIDK----PIVSGP---LFDM\n+RC--EATINKNLKAIFKILKI--N----K--S-------------ISYHC\n+ARHTFGT-LYIYLGGEVTNLKEMMAHSKIDTT-M-V--YVGMAKRLTINE\n+KRLFDEEFASDMKVILKGKG-E-------------------IMEA-V---\n+--------------------------------------------------\n+--------------------------------------------------\n+-----\n+>761193.Runsl_1261\n+--------------------------------------------------\n+----------------------------------------------MFDV\n+FFKLRYRRNRD--G----------QPDHEVPASLVYFVR-------IDGV\n+RSN--EKSTGIEVLKSKWKSKFQKI---------EGTSEE-V-Q------\n+----------MMNKRISLIRAGLDRIHQELCFIHDYVTAQQVLDVY--VG\n+KA---E-K------------------QATILKVFDAFLAELK----EPKK\n+KETI-KIKKKTFEKWEKAREHIESFLKKK-KMVVMPMSRFNSPL----AE\n+QYREYLYA-CG--------------------------FQKDHVSRNISYL\n+KKVFKEAKR-TGLIHENPI-KDVPC-PRSRHKN-AIPLETTEIQRLL---\n+EFSSD-NT-ILQQSADIIVFMCFTGLDYCDYIRFNPKEHL-KVIDGANMI\n+QIHRQKNERGGIVP-KLVNIPIL-PEAQEILDKYNNLP----------PI\n+LK-Y-HTIRRNLLIILRNIGVD--------KP-------------MSLKN\n+LRKTFGT-YLLNSGLRIELVRDALGHETIALT-E-RVY-TIIYPETIVQD\n+F-----------KK-NGLI-------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----\n+>880070.Cycma_4293\n+--------------------------------------------------\n+------------------------------------------------M-\n+-KVTL--R--K--R----------NQGGK--TSLYLDYY-------HKGK\n+R-KTEY--LKLYLSP-------------------NAKTKEE--K------\n+----------EVNKKTLQLAETIRAQRQIEIQNGVY--------GF--RD\n+NE---KL-------------------KGSFLAYIELLA-N-Q----R---\n+---Q--DSPGNYGNWTSMLKHLKAFCSY-----EVSFSDIDRQFIQDF--\n+--KYYLDKKAIA--HG----DQ----------KL--SQ--NSKYSYFNKL\n+RAALKQAVK-DGILPTNPSE-GVDAFKQGEP-E-REFLTLEELQAAA---\n+NTECE-----IPQMKTAFIFSCLTGLRWSDINKLLWSEV-QHSNDNGYYI\n+RFRQK------KTK-GAETLPIS-EQAFGLLGERQAPEERV------FKG\n+LK-YSAWHNLKLQQWMMKAGI--S----K--T-------------ITFHC\n+ARHTYAT-LQLTAGTDIYTVSKLLGHKELKTT-Q-V--YAKIIDEKKQEA\n+A-----------NK-IKLDL------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----\n+>504472.Slin_5336\n+--------------------------------------------------\n+----------------------------------------------MKV-\n+-T--L--RE-K--P----------INDGK--ISLYLDFYPAISHPETGKD\n+T-RREF--LGLYLFD-------------------KPRTELD--R------\n+----------QHNKATKLLAQNICATRQLEVQAGNY--------GF--LK\n+KK---VV-------------------AVDFLAYFKKQA-DIE----K---\n+---A--RDKGSRNNWNSAYLHLYNFTTG-----KLTVDEVTADFCKSF--\n+--RDYLTTAKPLNVTKSA--KK----------AI--AH--NSAKGYFVIF\n+GTALNRAVD-DKLFTINPND-TVKGLTRKET-Q-REFLTLAELQSLA---\n+KTECD-----LPYLKRAALFSALTGLRYSDVAKLTWSEV-YEDVNGS-YI\n+RFMQQ------KTE-GVETLPLN-ETARILLAERSE--GVV------FPE\n+LL-YSSWQNQKLSEWAHRSGI--K----R--R-------------ITFHA\n+FRHTFAT-LQLMEGTDLYTISKLLGHRNITTT-Q-I--YAKIVDTQKRAA\n+V-----------NR-LSIEI---------------------T--DMN---\n+--------------------------------------------------\n+--------------------------------------------------\n+-----\n+>880070.Cycma_3334\n+--------------------------------------------------\n+------------------------------------------M---EATL\n+RLELR--KD-K--V----------NRNGE--HPLILIIR-------VAGQ\n+R--RKM-GTSIKLHPELWDNDNQKII---------NLTQK-LKVQLQKSY\n+GDTITKNQLIQNQEELNSLIIRIKTIESKFIYEGIPYSADMIIEIL--KE\n+SK---A-AKTKKEDP-----------TNLVYDFIDRYIQEHE--------\n+---L-TRVKGSLVVYKSLKRHLKNYQTK--TKVNFRFDKVDYNFMQSF--\n+--QNFLIGW------------EEVHETTGKVRTL--NN--ITIAKQLSTL\n+KTFLGYAKR-QGIKVNGGYK-DFTI-KKEKLE--VIALTQAELELLF---\n+NFNLSLNK-RLDQVRDVFCFSCVTGFRFSDLQQLRREHIK------EREI\n+RLTI'..b'----HETILTLFQKHNDDVK-QLVG---\n+--IS-K-TIATYRKYEVTRRHLAEFIQSKYNVSDISIKEISPMFITDF--\n+--ELYLRTA------------C----------KC--GY--NTTAKFMQFF\n+KRIIIIARN-NGILVNDPFA-SYKI-RLEKVD--RGYLTEDEIKIIL---\n+KKKMV-SE-RLEHVRDLFIFACFTGLAYIDVAGLTQDNIR-KSFDGNLWI\n+MTKRQ------KTN-TDVNVPLL-DIPKMILKKYKGKL---PNGK-ILPV\n+IS-N-QKLNAYLKEIADICGIK------K--N-------------LTFHL\n+ARHTFATTTTLSKGVPIETVSKMLGHTNIETT-Q-I-Y-ARITNSKIGSD\n+M-----------QG-LDKKFVG-----------------I--EKIYKEVA\n+-M------------------------------------------------\n+--------------------------------------------------\n+-----\n+>435590.BVU_2470\n+--------------------------------------------------\n+------------------------------------------M-KSTFSV\n+LFFVK--KD-K--Q----------KINGS--YPIFVRI-------TIDGV\n+A-S-RF-NSKLDVQPKLWDGKAGKA---------AGRSAE-A-T------\n+----------RINRLLDDINASLNTIYHELQRRDNYVTAEKVKNEF--LG\n+HS---E--------N-----------HDTILNLFQKHNDDVK-QLVG---\n+--IS-K-TIATYRKYEVTRRHLAEFIQSKYNLSDISIKEITPMFITDF--\n+--ELYLRTT------------C----------KC--GY--NTTAKFMQFF\n+KRIILIARN-NGILIGDPFA-NYKI-RLEKVD--RGYLTEDEIKIIL---\n+KKKMV-SE-RLEQVRDVFIFSCFSGLAYVDVANLKEDNIR-KSFDGNLWI\n+ITKRQ------KTN-TDVNVPLL-DIPKMILEKYKGKL---PNGK-VLPI\n+IS-N-QKLNAYLKEIADVCGIK------K--N-------------LTFHL\n+ARHTFATTTTLAKGVPIETVSKMLGHTNIETT-Q-I-Y-ARITNNKISND\n+M-----------QG-LDKKFVG-----------------I--EKIYKEVS\n+-MK-----------------------------------------------\n+--------------------------------------------------\n+-----\n+>762984.HMPREF9445_00225\n+--------------------------------------------------\n+------------------------------------------M-RSTFKL\n+LYFVK--RN-A--V----------KKNGN--APIIARI-------TIDQV\n+V-A-QF-NTKLEINPAHWSVKLGKA---------SGRTAE-A-V------\n+----------HINSMLESIRSTVHQHYHALMAQDGYVTAELVKNAF--LG\n+KI---A--------R-----------ERTLIEFFKQHNEQYL-QKVK---\n+--MN-T-TDKTYSRYELTKKRLIEFMKFKYSVSDMLIKDINVVFIEDF--\n+--LLYIKNN------------Y----------GC--SH--NTAMKFVQRF\n+RTVVNFAKN-TGLVTADPFG-SYRV-KFERTD--RDYLTMEEITAIY---\n+NHKFC-TK-RLEQVRDLFIFSCYTALSYIDVCELRQEDIR-TGFDGNLWI\n+IRKRH------KTN-VTSTVRLL-DIPKAILEKYKDKL---PNGK-ILPV\n+IS-N-QKMNDYLKEIAAICGIE------K--N-------------LTYHV\n+ARHSCATSVLLSNGVPIETVSKILGHTNIRTT-Q-I-Y-ARITDLKVSND\n+M-----------EM-LAQKLDA-----------------T--HRTASR--\n+--------------------------------------------------\n+--------------------------------------------------\n+-----\n+>226186.BT_2277\n+--------------------------------------------------\n+------------------------------------------M-KSTFKT\n+LFYLK--KN-E--P----------KKNGH--VVIMVRI-------TVDGD\n+Q-V-QF-SSKLDIHPDNWDTKTGRA-VINKQSADKKENLR-V-S------\n+----------SLNKTLDEIRSAITMHYTRMMNVDGYALPEKIRNAF--LG\n+LE---E--------K-----------EKTLISYFTQHNEQYA-KKVG---\n+--KT-A-TQKTYSRYELTKQRMIEFLQKEYKLSDIPVKEITVTHIENF--\n+--YLYLRQE------------C----------EV--SN--NTAMKFVQRF\n+HTILLFAQK-SGLSFIDPFG-NFRF-NFDKTD--RGYLTQEEIDTIY---\n+YKEFK-SK-RLEHVRDAFIFSCYTGLPYCDIYTLSSEDIK-IGVDGKKWI\n+MKDRG------KTG-VESFIPLL-QIPLDILAKYEGKL---KDGR-LLPV\n+IS-N-QKMNEYLAEIAAICQIN------K--R-------------ITYHL\n+ARHSFATEICLTKGVPIESVSKMLGHTNIQTT-Q-I-Y-ARVVDRKLSHD\n+M-----------NM-LDRKLKN-----------------M--QKGTTQNA\n+-V------------------------------------------------\n+--------------------------------------------------\n+-----\n+>742767.HMPREF9456_03208\n+--------------------------------------------------\n+------------------------------------------M-KSTFRT\n+LFYLR--KN-Q--P----------KSNGM--YPIMLRI-------TINSK\n+V-T-QF-STKIDIHPNQWDAKAGKA---------KGRTEE-I-A------\n+----------EINRKLTNLSSRIDKAYNKRMEENGYALPEEIKNDL--LG\n+TD---T--------A-----------HKTLIYYFTKHNEQYQ-QKVG---\n+--KN-T-TYTTYKRYELVKTRLIEFLSEKYNLTDISIREMNTILLEDF--\n+--YLYLRNK------------S----------EI--NN--NTAMKFLQRL\n+RRVINFIIKGHGETIPDPFI-NFKF-HYDEVE--REILTLDEINTIY---\n+TKVFA-SK-RLSQVRDIFIFSCFTGLSYIDVFNLAESNIQ-QAFDQSLWI\n+MTKRS------KTG-VKVKVRLL-DIPYKILEKYKGKQ---KNGK-VLPV\n+IT-N-QKMNDYLKEIAAICNID------K--T-------------LTFHI\n+ARHSFATSIALSNGVPIESVSKMLGHKDIKTT-Q-I-Y-AKITDLKVSKD\n+M-----------ED-LSKRIN------------------M--KVG-----\n+--------------------------------------------------\n+--------------------------------------------------\n+-----\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,4305 @@\n+>309807.SRU_0046\n+---MAADISQSKYTNVIDLTSEAQQERR-R-----------DEVG-----\n+----SELREPDPPLD-EVTVDELSGHMEQAVHAAGWTELMDVQRKAIPYT\n+LDGRDLIVQSQTGSGKTGAFLLPLFDLVN-------------P-DK----\n+--------EEQQVLILTPTRELARQIHEEFEQMKIATPRTNR-MEAVLIY\n+GG---VGYQPQIDGLKNGAQVVIGTPGRILDHIKKDNFDASTLRMLVLDE\n+ADEMLSMGFYPDMKDIVEHVPGDRVSYMYSATMPPKVRSVAREFLD-DPG\n+FLSLS---TDKVSVEENEYRYYLVNPM-DKDRVMAQLLEL---E-E-PES\n+ALIFANTKREVSYLNKFLSNK--G-YDIDEMSGDLSQRDREEALDRLREG\n+KLRLLVATDVAARGIDVSDLSHVFIYDVPQDHEYIIHRSGRTARAG-EEG\n+TTIVLSTHEDEYELKRMANTYDIELEKA-ELPAD---------P------\n+-HS-E--ARELLQ-----E-R-YANAEA---------------PANGEEP\n+G-------------------------------------------------\n+----VED-----------FVPL-VKE---LS------------------D\n+EQP-E-----------------L---------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------LA-----------SI--ITELY---------------------\n+--------------------------------------------------\n+---------------------AEAKTE----DE------EEK--------\n+---------------------------------------------\n+>452471.Aasi_1916\n+--------------------------------------------------\n+-------------MT-NFQEMGLSPVLTQALDKLSFTQPTAIQAKAIPLA\n+LQQKDILGSAQTGTGKTLAFAIPLINKLL---------------S-----\n+-------DPTSMGLILTPTRELAQQVATNINQLLFK---S-SFIKTALLI\n+GG---EPYNKQLAQLRSNLRIIIGTPGRVIDHLERGSFNPKDIDFLILDE\n+TDRMFDMGFSIQLEQIVSQLPTQRQTLMFSATFPPKVEKLAAKYMQ-SPE\n+RIFMNEFDSMAIVAQNLTQEILEIKEENKYFELLTQLNSR-------EGT\n+ILVFVKTKDNAEHLSLRLNKE---AYNTCAIHGNLRQTKRERVMRAFRQG\n+RHQIMVATDIAARGLDVPHVKHVINYDIPHAPEDYVHRIGRTARAG-AKG\n+FALSFVSSQDRKRWNAIQDLLNPKQAKS-DRNSE--QHGS--RNR----N\n+SRNNN--SRPRSQ-----S-M-DSS-RG----------------------\n+--------------------------------------------------\n+------S-----------ERDR-FQK---SF------------------P\n+SSR-N-----------------GGSSEFSRS-R-SQG---MG-S---AR-\n+------DSERDRFQR-SSASSRHGESSDFSRPRLQGTDSP-R--DF--Q-\n+RDKFQRSSTP---------------FRHSESSEFS---RSRSQGTNSL--\n+------------------------------RGSE--R--D----------\n+-----------------------------------RFQKS----------\n+--SSPSRYGGNPEFSKFRSQGSDSTKR----SFQEKGGQKAFSPSR----\n+-RIEAAPEF-SNKG-FN-K----KKFSDKKRYQ------------\n+>760192.Halhy_0167\n+--------------------------------------------------\n+--------------M-NFTEFGLHPDLLDGVDAMNYKTATPIQEKAIPII\n+LEGKDLIGIAQTGTGKTAAFILPVLNEIIESG----------E--A----\n+--------NFIQTLVIVPTRELAVQIDQVIEAYSYF---T-G-VSSIAIY\n+GGGDGKEFAQEKNALVSGVDIVIATPGRLISHLNMGYVNFSKLRFLVLDE\n+ADRMMDMGFQPDLMRIIGKIPQKRQTLLFSATMPESVMKLARQLTH-NAE\n+SVSIA----LSKPAEGVTQRAYVVYEE-QKLQLVTELLKD---R-K-GQR\n+IVVFCSSKASVSSLYSKLHRK---NLSVGQMSSDVEQDQREETMLAFRNS\n+KIDIIVATDVISRGIDVDGIDLVVNYDVPRDPEDYVHRVGRTARAE-RKG\n+EAITLVSPGDQLRFRRIEKLIDKDIEKL-GPPQN--L--G--PGP-----\n+-EY-A--PNARR-----GK-T-FGPPHR---------------QANAQGK\n+GGN-----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------------N\n+Q-HSN---RS--------NSGGG----------G-----GGPHKKKSGSG\n+SSRWN-------NKPK-----------PS----------G-----E----\n+---------------------------------------RTE---PR-RD\n+V--------------------------------------------\n+>700598.Niako_6714\n+--------------------------------------------------\n+--------------M-RFTEFGFHPDLLEGIEASNYENATPVQEQVIPPI\n+LAGRDIIASAQTGTGKTAAFLLPVINRLLTHR----------I-DG----\n+---------QVGALVIVPTRELAIQIAQHLEGLSYF---T-N-LSSIAVY\n+GGNDGSNFVAEKKALQTGTDIVVCTPGRMIAHLNMGYVQFKQLQFLVLDE\n+ADRMLDMGFSDDLNKILGTLPTQRQTLMFSATMPDKIRQLARKILT-NPA\n+EINIA----ISKPPEKIVQKAFVVYEP-QKLPLLKHILTN---V-P-FKS\n+ALIFCSRKQSVKLLVRDMERA---KFKIAEIHSDLEQSQRENVLNGFTSG\n+RIPILCATDILSRGIDIDTIDLVINYDVPRDAEDYVHRIGRTARAE-ADG\n+MAFTLVSEAEQNKFAIIEKLIGKEVEKA-VVPEE--L--G--STP-----\n+-AY-Q--PRLRS-----KS-------------------------------\n+GGN-----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------'..b'-VRHGVIF\n+GG---VNQRPQVDMLHKGIDILVATPGRLLDLMNQGHIHLDKIQYFVLDE\n+ADRMLDMGFIHDIKRILPKLPKEKQTLFFSATMPDTIISLTNSLLK-NPV\n+RISIT---PKSSTVDAIEQMVYFVEKK-EKSLLLVSILQK---S-E-DQS\n+VLVFSRTKHNADKIVKILGKA---GIGSQAIHGNKSQAARQLALGNFKSG\n+KTRVMVATDIAARGIDINELPLVINYDLPDVPETYVHRIGRTGRAG-NTG\n+TALTFCSQEERKLVNDIQKLTGKKLNKAS-YTI-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------\n+>226186.BT_1885\n+--------------------------------------------------\n+--------------M-TFKELNITEPILKAIEEKGYTVPTPIQEKAIPVA\n+LAKKDILGCAQTGTGKTASFAIPIIQHLH--LNKGE--------------\n+-----GKRSEIKALILTPTRELALQISECIEDYSKY---T-R-IRHGVIF\n+GG---VNQRPQVDMLHKGIDILVATPGRLLDLMNQGHIRLDNIQYFVLDE\n+ADRMLDMGFIHDIKRILPKLPKEKQTLFFSATMPDTIIALTNSLLK-NPV\n+KIYVT---PKSSTVDSIKQLVYFVEKK-EKSLLLISILQK---S-E-DRS\n+VLIFSRTKHNADKIVKILGKA---GIGSQAIHGNKSQAARQSALGNFKSG\n+KTRVMVATDIASRGIDINELPLVINYDLPDVPETYVHRIGRTGRAG-NAG\n+MALTFCSQEERKQINDIQKLTGKKLNRAD-FTI-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------\n+>886377.Murru_0576\n+----------MHYN-KKHRTGT-------------SGKRPVSRLNPELLV\n+KKSTSTNTEPYVS-DRNFEQFHLHGELRKNIAHKGYRSPSEIQDRCFDHL\n+LKGKNLVGIAATGTGKTGAFLIPMVQQML--T------------------\n+-------ANNVSGLVVVPTRELAQQVQSEFRSLTKG---TR--LTSACFI\n+GG---TNVGRDISSARGNLDLIVGTPGRLNDLIDRRALRIDTRSTLVLDE\n+FDRMLDMGFIKDIQKLVSGMRNRKQTMLFSATLDPNQEKLIQQITG-AAT\n+RVNVS---SGTRSSDNVDQHIIRVKNSENKFDVLFKLVNES----S-FEK\n+VLLFAETKRGVDKLSKQLKNS---GIRSDVIHGNKSQNYRSRAIELFKSG\n+STKILVATDVAARGIDIKGVTHVINYQLPQTMDSYIHRIGRTGRAS-ATG\n+VAYTFVN-------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------\n+>388413.ALPR1_08353\n+----------MERNTNRNRTAKPQGARRPQRGPRQTQKKKESTLDPNLLV\n+KKAKPSGQEGFQSKT-SFASLSLDSVMMRNLSEKGYENMTNIQEQSIEAL\n+LEGRDLLGISNTGSGKTGAFLIPIIEHAL--KN-----------------\n+-------PGQFTALIVTPTRELALQIDQEFKSLSKG---MR--LHSATFI\n+GG---TNINTDMKVLSRKLHVIVGTPGRLLDLTNRKLLKLNQVKTLVLDE\n+FDRMLDMGFVNDVKKLVGGMTQREQTMLFSATLEPNQKNLIQSLLK-NPV\n+EVKIN---TGVSTNENIEQGIIRVPEGKDKFGMLADLFQNR----A-MDK\n+VIVFTETKRLADRLSKKLNQA--G-VKSGLIHGNKSQNFRNKTIEQFKSG\n+ETRVLVATDVAARGIDVADVSHVINYQLPMTMDSYIHRIGRTGRAG-KTG\n+HAITFVN-------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,7831 @@\n+>487796.Flav2ADRAFT_0517\n+--------------------------------------------------\n+--------------------------------------------------\n+-------MKN----FLKA-I---I------I--CC----LLTQ-CQS---\n+P-----------------------NRIATPIVFTINAFDVPNNQMEVTFS\n+ITNTTDTFWEGGNWSLHWNSIFGETIP-ESL-PEGMEYNYVDGQQYLILT\n+FGEQYNLNPKESLSFSAVQKGIIPRLAMGPNGFFVHNK--NTQTNIDLES\n+KIV---------WQNAKGIEGLNIPSAEDRYAT-YKTLKTVP-K------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------EQL-AWVIPSP\n+QKH----E-F---K---G--E--Y-----RTPSALNFNL-----DSF--E\n+MDVNFISER--LQE-----G--LTI-T-------VNSE---NN-------\n+--------LD---NNLSV---------I------Q---------------\n+----N---------NSL-GRE-AYRLQISE--DKIRIEAS-HSTGVFYAF\n+ESLHQILL-IAQ----------------------------NEEK---GW-\n+-PIITIEDAPRFENRGFMSDVARNFYPKEKLFQILDYMALYKLNRFDLKL\n+TDDDGWRIEIPGLPELTEVGGKR---GYTKD-----E-NDRLIPMYGSGS\n+G-----------------------------------------DQ-K----\n+---S---TGNG--FLSGQDFVEIIQYAKERHIEVIPQVSFPSHARAAIKA\n+MKARYENYKAA-----GDMEAAT---------------------------\n+-------------E----YMLHDPEDQSE-----------Y---RSAQLY\n+S---DNVVCICDDSAYRFYEKIILEIKALYEKADTPMKVFNIGADELP--\n+-YGPWQKSPKCKEYIANNKSIPS------VK--------------DLYNY\n+NLRLINTIIT-NAGARMVGWEDAL----LVHSE-NEQ---SELN------\n+-----IKEDL----LDLDFTPYVWN-----NT-WG--GGREDMIYR----\n+-----------------------L-ANKGFKAIMSNS-SAFYFDMVDDYD\n+M-E-N------YGM--SW-S--GYVTYKDSWGTEPL-NVF-A--------\n+---------------NKVKLEALGIDEATVTT---KEFLKPE--AKDNFL\n+GIQSQLWTET-ITSE-----AVFDALLMPNLIVFSQRAWGAKE-PWIDLP\n+TASDQKPALEKAWNLF-VNNLG-QRQ-LPLINQLYGGVS-F-DLPKP-GG\n+--------------------------I-LK------------------EG\n+ELWVN------QQF-----PGLIIRYTTDGNEPTSESRKYTER-VKLPAQ\n+----SKVRLRSFDSRNRG------------------GK------------\n+-------SISIN--------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------\n+>657309.BXY_17860\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------M-M---L---------GI----CLFG-CGA---\n+G----------------------KQPPSSQLSLTWKLEKDSVEAMYFKNT\n+FCLTNNGNKSLTNNWVIYFNQTPIYYQ-QPI-NAPLEIECLGSTYYKMYP\n+TEHYQALPPGETITFTILSEGNVINVSSVPEGAYVVTTDEKGKPLQPQNV\n+PIEIELFK-PDVQW-VSSRNSFPYADGNYFYKQ-NDDFSKPV-D------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------CDM-LSLFPAP\n+KKV-E--K-M---G---G--V--S-----SFSQKVCLKFD----DAF--K\n+EEALLLKSQ--LTS---LLR--CNV-S-------DK-----DE-------\n+---------E---TIIELKK-M-E--VP------I---------------\n+----T---------CQY-PDE-YYEIVIKN--NRLTLKAS-DIHGIFNAC\n+QTLLALLD-NME------------------------------LT---SSS\n+LPNLHITDYPDMGHRGIMLDVARNFTKKADLLKLIDILSFYKMNVLHLHL\n+SDDEAWRVEIPGLEELTEIASRR---GHTID-----E-QTCLYPAYAWGW\n+N-------------------------------------ET--DT-T----\n+---S---LANG--YYSRSDFMDILKYAKERHIRVIPEIDIPGHSRAAIKA\n+MNARYQKYIDT-----DQ--SKAE--------------------------\n+-------------E----YLLTDFADTSQ-----------Y---LSAQNF\n+T---DNVINVAMPSTYHFLEKVIDEIVRMYQDAGVELTAFHVGGDEVP--\n+-EGIWEGSSICRTFMQEN-GLTK------IR--------------DLKDY\n+FLEQILEMLD-KRNIQAVGWQDIV----MNPDN-T---------------\n+-----VNEHF----KNSKVLNYCWN-----TI-PEQGG--DEVPYK----\n+-----------------------L-ANAGYPIILCNV-GNFYLDMAYCYH\n+--V-E------EPGL-RW-G--GYVDEYVTFDMLPF-D-I-Y--------\n+---------------KSLRRNLKGEPVDVKAASNGKQPLTKE--GYQNIK\n+GLSGQIWSET-IRSF-----EQVEYYLFPKVFGLAERAWNVQP-SWALSP\n+D----GKVYMDAKRKY-NAGII-DYE-LPRLA--KRGIN-F-RVSPP-GI\n+--------------------------M-IR------------------DG\n+LLLAN------TAI-----PNAVIRYTTDGSEPTESSIEWQTP-VVCNA-\n+----PLIKAKAFYLGKES------------------VT------------\n+-------TVLFN-R------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------'..b'---L----------ISA-V----LFS----C---\n+Q------KPLS---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------E-------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------LES-AAIIPLP\n+SSI-V--A-G----H--G--S--F-----ELNSGSAIQIIGN-SEGL--Q\n+GLGEVLASR--LKP---ATG--FD-LPV-------NAD------------\n+------------GGDIQLELLG-G--------------------------\n+-----------------EESE-AYTLVVE-E-DLIKITAN-SEAGLFYGI\n+QTLVQLFP-VAIEN------------------------NSITEA---SWT\n+VPAGKIVDQPEYGYRGSMLDVARHFFTVDDVKYYIDEMAKLKLNSLHLHL\n+TDDQGWRIEIKSWPNLTTIGGKS---EVG---------------------\n+--------------------------------------------------\n+---G-G--DGG--FYTQEDYKEIIAYAAKNYITVIPEIDMPGHTNAALAS\n+YGEL----NPG-VNLPDG--D--F--------------------------\n+-------------S--TMNEGEIDFDILDGDPKA-AEIYTG---IEV---\n+G---FSTLATNKEITYQFVEDVIREISEMT-----PGPYFHIGGDESH--\n+-VT-------------------E------KD--------------D-YIE\n+FVERVQKITA-KYGKTSIGWDEIA----TT--------------------\n+--------E-----LLKGNVAQFWA-----LA---------ENAKL----\n+-----------------------A-IEQGNQVLMSPA-KKAYLDMQYDST\n+--S-R------LG-L-HW-A--AYIELDSAYIWDPE--N-----------\n+---------------Y-D-------------------P--GI--KKQDIF\n+GIEAPLWTET-IETR-----EDLNYMVFPRIAAIAEIAWTPSE-------\n+---------KREWSDF-QKRIA-V-Q-GKRWDI--NGIG-L-Y-------\n+--------------------------------------------------\n+----------------------------------------KSPKVEW---\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------\n+>760192.Halhy_5983\n+--------------------------------------------------\n+-------------M-P-------------T---------NR-ITYYSAT-\n+L------L-----C-----A----------ALL-T----FMG----C---\n+A------PKKA--P------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------PISMD-------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------LAQ-ESIIPIP\n+VSI-K--A-T----N--S--S--F-----ELTDASEIYVQTG-SEEL--L\n+KIGQFLADK--LNP---STG--FD-FTV-------KAS---TA-------\n+-------I--PDDGNIYLSLKK-D--A-------A---------------\n+-----------------LGDE-GYTLSIT-P-ELVHLEAN-APAGLFRGV\n+QTIRQLLP-AKIEM------------------------SSKQEG---PWR\n+MASGTINDVPVYAFRGAMFDVARHFFSVEDTKRYIDLIAAYKMNVMHLHL\n+SDDQGWRIEIKSWPKLAEHGGKT---QVG---------------------\n+--------------------------------------------------\n+---G-G--KGG--YYTQEQYKDIVQYALDRYITIIPEIDMPGHTNAALAA\n+YPEL----NC----------------------------------------\n+------------------------------DGKA-RELYTG---TEV---\n+G---FSTLCTQNEITYKFIDDVMRELAAMT-----PGPYIHIGGDESH--\n+-VT-------------------K------KE--------------D-YIP\n+FVNRVQNIVL-KHGKQVIGWDEIA----LG--------------------\n+--------T-----LKKGAFVQHWA-----DV---------DNAVN----\n+-----------------------A-VKQGSKVLMSPA-RKAYMDMQYDST\n+--T-K------WG-L-HW-A--AYIEVDSAYIWDPA--T-----------\n+---------------L-A-------------------P--GV--TQKDVL\n+GIEAPLWSET-VDQI-----DEVEYMVFPRLPGYAEIGWSAAS-------\n+---------ARNWGEY-KKRLG-A-H-GPRFTA--MGIN-Y-Y-------\n+--------------------------------------------------\n+----------------------------------------PSKLVEWKEE\n+----KNQKN-----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,9792 @@\n+>760192.Halhy_5399\n+-------------------M------------------------------\n+--------------------------------------------------\n+------------------------------------------------RP\n+HNFK----------------------------------------------\n+----------------------------------A-C--F----L-VL--\n+------F-L-----------LGMAN------LQ---AQ------------\n+--------TT----------F----R-----------GLMRKADQLFETY\n+AFAPAVDVYRQA--LE---KD-----------------------------\n+AT--DPDALGRLAECYRYLN-RLDEAEATYLKLIRGRK----Y-------\n+---E-----------DRQILLYAHCLKGLGRYDEAKVYYLSYAKINP---\n+----TVG--------NQF-A----QS-CDF-AKA-N-LNLP-T-VYGLSN\n+---E--R-VNSSSSD-FGPAFL-N-D----QLVFSSLRT-----------\n+--E-----------------------G-Q-TFSSTKS-----S-LYSSV-\n+---------------MATD-----------------G-S-----------\n+-------------------------L-------QT---------------\n+---------------------------------PIV-VR----PG----I\n+S---DFSIGPATFSSDGRNAATTKN-NFT----P----G---V--RQI--\n+-PGS--GLDLSLILAD--VNFN-----S--------------SWYNERTF\n+PN-N-D-TKGRTGFPCLTPDG-----------------------------\n+---NALFFASDR--EG--------GFGG--------WDLYLS---YKEGA\n+N-WTKPINLGPAVNTPGDEITPYF--DGLN-LYFASDYH-L-GFGGFDVF\n+MA---E-----------------Q--G-E--------GR--WLK-STNLG\n+QPVNSSADDYGMIMD-S-----------YRNF-GYMVSNR--SGG----K\n+GM---------EDIYRVV--------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------KGGAP------------------------VVTD----\n+-----PG-NPNPVNPNTGRTRIKVFSGSDG-MALPNASVDL-----T--N\n+C-M------RG---SS-NYI----LLTD-------GQGYVELPVGAGTEC\n+EVVVRADGYMQLRGSLSAYFAPNRDIEIPLTKSGEEYYGRVVNSNTREFI\n+PNAQITARNTYTGTITRTTSDYSGNY--VL-S------LS-RN--TP-YT\n+ITY----SAP---NFNEE-----------T--RN----------------\n+---------------------I-----NVL-NG-S-DR-TV-------L-\n+GV--------------LSMVPNAWNP-N-PN-P-------VNP-------\n+-----------NPINP---------NPGNT-GTQLE--------------\n+--------------------------------------------------\n+------------------------RP---GF---------------AI--\n+------------------------------Q------VS----AVSGQ--\n+-PD-LSKFNNLR--SIASVY------------------------------\n+---------------------------AKNEAGKYKIKVGNFPTREEAQR\n+QLE---NVKRMGYTGAFIVTDDGFSLGGGTAVAPAVPDPNPPVTTNPPVN\n+TGGRFMIQLGAYRDPRS-FNGTRL-AGMG--TIQDRPRADLTVKLLCCFS\n+S--------A-----------A------------DAY-------------\n+--NALPRVQQAGFSGAFVVEDLNGQLVRAK--------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------\n+>269798.CHU_2606\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------------MK\n+YLAF----------------------------------------------\n+------------------------------------S---I---V-----\n+-FILTA-------F-----------------T----R-------------\n+---V---TAQNLDGIDKSLSL---------------SKMKTRARIAEETG\n+DIYTALFYYEEV--VR------------------------ND--------\n+S--SDLKALYQVAEMQRFTR-NYKAAEVTYGKIHEI---A-AAD------\n+---Y-----------PLAQYYQGLMQKMTGRYEDAKQTFSEFRKNSAALA\n+D-K-TFK--------AT-LARDIS-G-CDS-GIT-Y-RDFP-Q-NTQIKN\n+-A-GK-S-VNFPHTE-FSPVILDS---T--TLAFGSLR-I--D-------\n+-SVI--------------YYD-----T-R-GEHYEKQ--PVRQ-LY-EAK\n+-------K---VK-G-----------------------------------\n+--------------------------------------------------\n+-------QW-------------------V-E--KGL-L-----EA----I\n+NDP-AMDMGNFVYSPTTDRYYFTKC-TKNH--------------------\n+--HG--KVSCAIYYSE--R--------V-S-G----------KWSHPSKL\n+PD-PINIEGYTATQPTIVIDTTSSSAATTTPKNMPPRKTGGNKPVPKPVV\n+NTIEYLYFVSDR--PK--------GKGG--------LDIWYT-SYNASK-\n+KTWNEPTNL-AVANTPETECTPFYHVPTQT-LYFSSNGL-V-NAGGLDIY\n+KL---E-----------------K--D----G-----RRF-G-R-PENLS\n+FPVNSPQDELSFVLA-D-----------NAKT-GFFVSNR--PGG----T\n+PFFHETCC---DDIFSFEV-IP----------------------------\n+----------PP--------------------------------------\n+---------------------------------------------'..b'FS-------L------------------------\n+----P---A-T---------------------------------------\n+--------------------------------------------------\n+-----I-----IRIDG--------------------------FVM---D-\n+-----RE----------------------G-YGIPQATVRI-----A--D\n+E-Q-------G---LLATPI----VSTR-------D--------------\n+--------------------------------------------D-----\n+-----------------------GSF-V-L-E------IA-GS--NR-YV\n+LHA----SHP---DYLNQ-----------Y--MP----------------\n+---------------------L-----VT-DSA-T-ES-T------D-Y-\n+--------------L------------V-DF-Y-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------LA-----------\n+S------------------------------------------R---LH-\n+----------SE--QIHDIYYDFDRASLRLEGKKSLD-YLV---TLLE-Q\n+NPDVRLELSSNTDRKGSQRYNKRLSQRRAQSVVNYL--------------\n+--------------------------------------------------\n+------IA-------K-GIAADRLE-ARG--YGKERPYV------VTKGM\n+AT-RFDWLPE-----------G-----------Q-ELTAEWVGAL-T-E-\n+--EQQVVCDQLNRRTEFTVIQ-----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------\n+>879243.Poras_1679\n+--------------------------------------------------\n+------------------------------------------M-------\n+------------------------------------------K-----VS\n+SSHI----------------------------------------------\n+------------R----------------------W--L-L---V--LLP\n+CAMALC-------S-----------------L----M-------------\n+---S----CK----------S----------------VTLSKAELYDHTG\n+RYALAADSYYTL--YR---RTS----------------R--K------KP\n+E--RRAYLAFKAAENYRRLG-NTPRALNCYNLALSG--D--YP-------\n+---D-----------SILHLRIAQELQQLARWREAGKAYEQFLEYYPH--\n+--------D---YFGRI-GL---A-S-VRQ-ADS-L-LAHP-T-GHTVET\n+---DR--LLISPYAE-FAPCYA-P-D--GTTLYFTSSR-V--P----L--\n+-R-----------------DM-----L-Q-ESEVTGL--GTNN-LFM---\n+----IKQD---AS-G-----------------------------------\n+--------------------------------------------------\n+-------KW-------------------S-R--PDS-V-P---GS----I\n+N-T-AEDEGTPSITSDGNTLYYSYAE-Q-----S----------------\n+-STY--DRTVQIYKAS---------K-S-SQG----------GWGKGERV\n+PI-W-EDSLRMAAHPAIDA------------------------------S\n+G--RYLYFVSE----GAG-------LGG--------KDLYRI-ALSEHG-\n+--WGKPENLGNEINTPGDELFPTMVGDS-T-LYFSSNGR-V-GLGGLDLY\n+KAQ-MD--------------------S--------L-GG--W-Q-VTHLG\n+APMNSPADDYAITFAPKPQS---G----LAEE-GYLSSTR--GD--Q--R\n+GR---------PHLYRFS-------L------------------------\n+----P---A-T---------------------------------------\n+--------------------------------------------------\n+-----I-----IRIDG--------------------------FVM---D-\n+-----RE----------------------G-YGIPQATVRI-----A--D\n+E-Q-------G---LLATPI----VSTR-------D--------------\n+--------------------------------------------D-----\n+-----------------------GSF-V-L-E------IA-GS--NR-YV\n+LHA----SHP---DYLNQ-----------Y--MP----------------\n+---------------------L-----VT-DSA-T-ES-T------D-Y-\n+--------------L------------V-DF-Y-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------LA-----------\n+S------------------------------------------R---LH-\n+----------SE--QIHDIYYDFDRASLRPEGKKSLD-YLI---TLLE-Q\n+NPDVRLELSSHTDRKGSQAYNQKLSQRRAQSVVDYL--------------\n+--------------------------------------------------\n+------IA-------K-GIAADRLE-ARG--YGKERPYV------VTKGM\n+AA-RFDWLPE-----------G-----------Q-ELTAEWVDTL-T-E-\n+--EQQIVCDQLNRRTEFTVIQ-----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,32054 @@\n+>398720.MED217_05687\n+--------------------------------------M--N--IIRFAL\n+RKPIAIIVTVLALLYFSVLAIQKIKVDIFPEVEAPAIYIAMPYGGLSPAY\n+MDGFMSNEFQKVLVFVGGIKNM--EFK--SVQGLTLMKLSFYPGT-D-M-\n+A--QAQAEVATQVS--RAM-AFLPP---GAVP--PQVVRFDAGA-QPVGQ\n+LVFE---S--DQRSTGELQNLAITRIRPSFVNIPGISAPAPFG-GNVRTM\n+VINVKPEEMQAYGLTADKILEAVGKNNFPSPAGNVQIG-------NTNYM\n+APVNTLELGAE-DFMNTPIK-T--G---SGP----TVFVRDVAT---VTD\n+GADKTT-A-YA-LAN-------------G----------------K----\n+---RTVYLPIIKKADASTLAAINNLKDAMPML--S-D-ALPEDVSIKFVF\n+DQSTYIENALSNLLHEGILGAVLTGLMVLLFLGDKRGALIVVLTIPIAVL\n+TAIIMLYL------LGQTINIMTLSGLALSIGILVDEATVTIENIHQHFE\n+----MEK-TKQRAILDALLEISIPKLLILLCILAVLIPSF-MMVGIPRDM\n+FMPLSIAVGSAMIASFLASQTFIPVVANWIMKKH-P--------------\n+-----------Q-------KHSD---------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--TKKS--------------------------------------------\n+--------------------------------------------------\n+------------R---FDRF-K---GRYLKFIQQKE----------R-Y-\n+--KK---PIFF-GYLLV---------------------------------\n+---------------------------------VI-A--LS-G-V-----\n+--------------------------------------------------\n+---------LFV----------SIGTDILPPSGS-KDLQLRIKAPVGSAL\n+DQTEDYVLAVEN-HI-R---------------------------------\n+-EQIAPD-K--LE--ITSGFVGMH------SP-NT-PIN-PI-F-LF-T-\n+SG-SQEAILQFSLPESF-D------------------------------V\n+PV-DELKDDLRTS-LKNE----FPELQFTFEPMELVEKIMG-Q-------\n+--GYNTPIAIEVLGK--NLDQVTLYAHKITDAL--K----DENYL-TDVH\n+LNEPVDYPSISINVDRERVAQLGLTMREVSTALTTATSS-SRFVSK---N\n+VWVDPN--SGLVFQVQVQLPE-NQVNSLNDLQNLPLKP-GA---------\n+------------------------M--SPVLDDVAD-LSLATEPGQVNRK\n+GPNRFVTVTANTNHS------DLGSASRK---VRKI-LS--E-----L--\n+-----DA-----P-PR---GYSV-R-M-AGEVNVLSETL--SGLQSGLLV\n+AIVVIFLMLTAYYQ-SFKTSLVILG-IIPAVVAGSLLSLS-----LL-GS\n+-----------TLN-LQSYMGMIMAVGVSVSNAVLIINQSEL-FR-KE-K\n+L--------------ENAAESSLLAVASRFRPILMTALAMIAGMIPMALG\n+------------------LGDGGSQVAPLGQAVIGGLVFSTFTSLLVLPF\n+IYTIAYAN-TQP--K-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----KV-SLDP-D----D----------QH-SKY---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------YQ---\n+---------KN-----------------------LK-S------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------\n+>655815.ZPR_1803\n+--------------------------------------------------\n+-------MTVLALLYFSVLAIQKIKVDIFPEVEAPAIYIAMPYGGLSPAY\n+MDGFMSNEFQKVLVFVGGVKNM--EFK--SVQGLTLMKLSFYPGT-D-M-\n+A--QAQAEVATQVS--RAM-AFLPP---GAVP--PQVVRFDAGA-QPVGQ\n+IVFE---S--DQRSTGELQNLAITRIRPSFVNIPGISAPAPFG-GNVRTM\n+VINVKPEEMQAYGLTADNILEAVAKNNFPSPAGNVQIG-------NTNYM\n+APVNTLELSRE-DFMNTPVK-T--G---SGP----TVFVRDVAT---VTD\n+GADKTT-A-YA-LAN-------------G----------------K----\n+---RTVYLPIIKKADASTLAAINNLKDAMPML--S-D-ALPEDVSIKFVF\n+DQSTYIENALSNLLHEGILGAVLTGLMVLLFLGDKRGALIVVLTIPIAVL\n+TAIIMLYL------LGQTINIMTLSGLALSIGILVDEATVTIENIHQHFE\n+----MEK-TKQRAILDALLEISIPKLLILLCILAVLIPSF-MMVGIPRDM\n+FMPLSIAVGSAMIASFLASQTFIPVVANWIMKK-----------------\n+-------------------HPQ----------------------------\n+-------------------------------------------------'..b'------------------------------------------------\n+--------------------------------------------------\n+---------------------------D------------------E---\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------N-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------\n+>709991.Odosp_2536\n+---------------------------------------M-S--IYNTAV\n+NKPISTLMVFIAIMVLGVASYIQLPVDQYPKMDPPYLTVMATYPGANASD\n+IEENVTKILEDQLNSVDNLKEM--TST--SYDNLGVISLEFEWEA-N-L-\n+D--EASNDVRDAVD--KAM-QNLPD---DIDR--PTIMRFNTSM-MPILI\n+YAVT---A---DQSYPGIDKILDDKLITRLNRVDGVASVIVAG-APERVV\n+YVDLDPNKLDAYNLTLEQIGNKILAENKDVSSGNVKMG-------LMDYA\n+LRVEGEFAESD-QIKNIVLG-T--Q---NNK----TIYLHDVAV---VRD\n+TIKDIT-L-EQ-TIN-------------R----------------G----\n+---RGGVLMITKQTDANAVAVAKEAKKQLEL--AM-K-ELPSDINFQIIS\n+DNSDFIVKSINNLQETLMYASIFVVLVVFLFLGRWRATFIIALTIPISLI\n+VAFIYLFA------TGESLNVISLSSLSIAIGMVVDDAIVVLENVTKHID\n+----RGS-RPREAAKYGTNEVWLSVIVTTLVTVAVFFPLT-LVTGMTGIL\n+FKQLGWIVCITVCTSTLTAISLTPMLCSQLMR---I--------------\n+-----------Q--------------------------------------\n+-------------------------------------------------E\n+-K------------------T--------S----------------N--S\n+------K-------------------------------------------\n+--------------------F--S--------------------------\n+-FY-N----F-VSR-Q---LDRL-DSGYERLIRWVL----------H-H-\n+--KT---F-VIC-FMTA---------------------------------\n+---------------------------------IF-L--GS-C-------\n+--------------------------------------------------\n+--S------L--T----R----FIKTDFMPQND-QSNMTVYAKMQSGQRV\n+EETKRVALQIDS-MI-R---------------------------------\n+-ADI--P-E--I-TI-INLSYGSE------EEASF-A-S--M-M--N-S-\n+T-GNNILNMRLRTVDIKDR---------------------------E--R\n+SI-FVIADQVRSI-LKSF----PDVLQYTVSTSSSG----G-S-------\n+--MGSNSVDIEIMGH--DFNTTTRLAQDIAVKA--R----QIPGA-EDIK\n+ISRDDDKAELQIALDQDKLARHGLTTSEVGSYVRNRIYG-FR--NS---K\n+FK--E---DGEEYDIIVRLDE-KYRSSLTEIENILIID-GH---------\n+------------------------G-EKIRLKELGE-IKEYFSPPNIERK\n+SKQRILKVSITPAA-G-------VALGDIAQASQQI-ID--N-----L--\n+-----ED-----V-PQ---DVSL--YI-GGNYEDQQESF--SSLIWLLLL\n+SLMLVYIVMAAQFE-SFKMPFIIML-AIPFAFTGVILALL-----LT-NT\n+-----------TLS-IVAALGAIMLVGIVTKNGIVLIDFINL-MR--E-R\n+G--------------IRLYDAIAQACRSRLRPVLMTSLTTILGMVPMAIS\n+------------------AGEGSETWRPMGIAVIGGMVFSTIITMIIVPA\n+VYAAMDKS-GSR--D-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----KK-KA----LA-KE----------FK-FMK-----D-------F-\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------D------------------P---\n+----------------------------E---KD----------------\n+---------------------------LP-------------K-------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------K-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,12238 @@\n+>702438.HMPREF9431_01410\n+-------------------------------------MK-K---------\n+--SF--I---------------------L-L-------------------\n+---------T-------AA------TL--L--------------------\n+-----------------------------------------------A--\n+----A---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------TS-GLTQQ--KF-KETKKGIYTLIEQKGGPTLGY\n+SPA-SGVK---IL-------------------------------------\n+--------------------------------------------------\n+---------------------------T---------------------V\n+GGFKF-KDLNRNGKLD--------KYEDWR-LSF--DE--RAADLASQLS\n+DEEIAGLMLYSAHQQ--I-P----AKSTGYG-ASTY--------------\n+-----------NG--------KPFEE--SGM-K-PS------A--L----\n+S---------------------DAQ-----------------------KK\n+F------LKDDYL---RAV------------LVTKVQSA----EVAAEWS\n+N-NLQ-SYC-ESFGHGIPANNSSDPRHEVSAN----AEYNYGAGGD-I--\n+--SQWPTALGLAATFSPELVKAFGKVAAMEYRALGITTALSPQVDISMEP\n+RWTRFTGTFGEDPALVADLSRAYIDGFQTS---T-GNKVIKDG-WG---Y\n+ASVVAMAKHWPGGGTLEGGRDS--------HY---NYGKYAVYPTHNFQK\n+EMQGFINGAFK-LAGPTKKAGSVMTFYN-ISYGQDPSGKNVGESFSHYIV\n+TDLLRHQYGFDGIVCTDWMVTKDNK-AI--DAFDGKCWGVENLSEVQRHY\n+E----------------ILKAGVDQFGGN--------NEKGPVLEAFKLG\n+YQEFGHEKWAQRIHNSARRLLLPMFETGLFE-NPY--LDPLK-SKAIVGN\n+REFMLKGYQAQVKSIVMVKNHR----------HTLPLKDAR--MKVYIPK\n+-RHFPSVTDFFGNKTRDYWD----YPV-----------------------\n+------------D-------------------------------------\n+--------------------------------------------------\n+--------------L---KLMSTYYQVVDTPQEADFALCFIQDPMAG---\n+-------------------------TGYSRADAEAGGNGYVPISLQYHDY\n+TATDARAKSLAGGDPKEA-----FTNRS--------YRGKTVKTANKDD-\n+--LLMVIDTKKAMGSKPVIVAITISRPAVFAEFEP-YSDAILVSFGTGK-\n+--RPFLDLISGKNEPFGLLPCQLPRDMKTVEMQAE--D------------\n+----------------------------------------------RPR-\n+----DMIPYTDS--DGN-QYDFAFGLNWSGIICDS---------------\n+--------------------------------------------------\n+RV-----KQYK---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------\n+>908612.HMPREF9720_1373\n+-----------------------------MTTKTD--LV-R---------\n+--RI--V---------------------SLA-------------------\n+---------F-------M-----L--P--I--------------------\n+-----------------------------------------------L--\n+----C---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------AC-G---R--KWTV-EPHDTYCLIRQDGGQTLGY\n+FPG-SGVR---IL-------------------------------------\n+--------------------------------------------------\n+---------------------------Y---------------------S\n+DGYAF-K'..b'AVAKSADVAILF-----------------IGSNREY---\n+-------------------------ES----E------------------\n+----------------GG------DRKN------LDL-----PFGEQQLV\n+DA---VTAA-----NAKTIIVVIGGAPYDLNKIKK-NNQTILWSWFNGSE\n+GGNALVDVLTGKVNPSGKLPFTFPASLNDSPAFALNT--YP-GDDL----\n+-------------------------------TAN----YK-ESIL-VGY-\n+----R---WFDTRKIE-PLYCFGYGLSYTDFNYAGLKTD----KKKYN--\n+---------------LNDKI--IVSLDLKNSGLLAGKETVQLYVNKPN-A\n+KVM-MPEKQLKAFTKVN-VESGKISKVAMALKVK-DLAYYNIEKKEW---\n+---VVEPGE-YKLMVGSSS------RDIRQ--------------------\n+--------------------------------------------------\n+--------TV-----------------------TV---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+NVN-----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------\n+>376686.Fjoh_0775\n+-----------------------------------------M-K-N----\n+-KM-------------------------I---------------------\n+---------Y----LSA-A----LVF------------------------\n+-----------------------------------------------AF-\n+-F-T----------------------------------------------\n+----------------------------S---------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------CK---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------NETQTS----------\n+------ASNSSQT---EEY-----VGKEIS-TDH--DA--EIDKLISQMT\n+LEEKIGMLHGNSMFA--N-A------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------G--VKRLGIPELKMADGPLGVREEISRDNWAPAGWTNDFA--\n+--TYYPAGGALAATWNAEMAHTFGTSLGEELRARDKDMLLSPAINMVRTP\n+LGGRTYEYMSEDPFLNKKIAVPLVVGLQE---------------------\n+KDVMACVKHYAA-NNQETNRDF--------VD---V----QIDERTLREI\n+YLPAFE-ATVKEA-----KAYSIMGAYNK--------FRGEYLCENDYML\n+NKILRDEWGFKGVVVSDWAAVHS-------------------------TA\n+KSLKNGLDIEMG-T---------PKPFNEF-------FLADKLIAAVKSG\n+EV------SEKEIDLHVKRILRVLFQVKAMG------G-GE-RAKGSIAT\n+EAHYQDAYKIAAEAIILLKNEN----------NALPLKL-DGVKSIAVI-\n+GNNATKKN-----ALGGFGA----GVK-----------------------\n+------T-----K-REVTPLEGLKNRL-PSSVKINYAEGYLEKYEEKNKG\n+NLGNI-----T------STG---PV----------------TI---DKLD\n+-PAK-VQEA-VEAAKKSDVAIIF-----------------AGSNRDY---\n+-------------------------ET----E------------------\n+----------------AS------DRRD------LHL-----PFGQEELI\n+KK---VIEA-----NPKTIVVMIAGAPFDLNEVSQ-KSSALVWSWFNGSE\n+GGNALADVILGKVNPSGKLPWTMPKQLKDSPAHATNS--FP-GDK-----\n+-------------------------------AVN----YA-EGIL-IGY-\n+----R---WFDTKNVA-PLYPFGYGLSYTTFALDNAKTD----KDSYA--\n+---------------QNDVI--EVTVDVKNTGKVDGKEVVQLYTSKSD-S\n+KIT-RAAQELKGFKKAD-VKAGGSEKITIKVPVK-ELAYYDVAAKKW---\n+---TVEPGK-YTIKLGTSS------RDIKK--------------------\n+--------------------------------------------------\n+--------EI-----------------------NF---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+TIK-----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,2600 @@\n+>575590.HMPREF0156_00530\n+-------------------------M-FDLAIIGGGPAGYTAAERAAHNG\n+LNVVIFEKK-AFGGVCLNEGCIPTKTLLYSAKLYHNAKNGS-KYGIG-TE\n+---NTTFDYEKIVSRKNKIVRKLNAGIRAKMTNCGATMV-VGEAEIKQHT\n+D-EKVVI-------L-AN--EQEFEAKN--LLLCCGSEVAIPPIKGLQT-\n+----------TEYITSREALELKAVPQSIVIVGGGVIGMEFAGLFNTLGS\n+KVSVIEMANE--ILPPVDSEIAAMLHAEYQK-QGIDFFVGAKVAELHNN-\n+------K-----V----LFTD----NQ-GNEQSIDTEKILLCVGR-KPSL\n+KG---IEILDLEPFR-NG--IKVSD-KMQTSKANIYAAGDITAFSMLAHT\n+AVREAEVAVNNIV------GK-S-DTMAYNAVPAVVYTNPEVAGVGLTED\n+ELKAQGR---SYSVRKLPMTFSGRFVAENEGGNGLCKLIFDDR-NT--IV\n+GCHMIGNPSSEIIAVAALAIE-QQ----LTSERFEKLIFPHP-SVGEIIK\n+ETLFA---------\n+>694427.Palpr_2286\n+--------------------------MYNLIIIGGGPAGYVAAERAGHKG\n+LSVILFEKN-AMGGVCLNEGCIPTKTMLYSAKTYENALHGD-KYGVY-GD\n+---NVRFDYGKIVARKNKIVRKLVAGVNAKMKQHEVMVV-SGEAIIQGKT\n+N-EGIEV-------T-CG--GETYLGEN--LLICTGSEAFVPPIPGLEE-\n+--------AGEIILTNREILQLKEQPASLVIIGGGVIGMEFASLYNSLGT\n+KVTVIEMLPE-I-LGANDAEISAMLREMYAK-KGIEFHMEAKVVKVEGN-\n+----K--V--------I--FE----KE-GVTESVEGDKILVSVGR-RAIT\n+KGFG-LENLQVELIK-G-G-IKVDE-KMRTNIPNVFAAGDVTGFSLLAHT\n+ASREGEVVVNNLT------GR-E-DKMRYDAIPGVVYTNPEVAGVGETEE\n+SATAKAI---AYKVAKLPMTFAGRFVAENEGGNGLCKVLVAEATDK--VI\n+GVHMLGNPCSEMIYGACMAIE-KG----MTLAELQEVVFPHP-TVSEIFK\n+ETVFAF--------\n+>203275.BFO_3055\n+--------------------------MIDLAIIGGGPAGYVAAERAAARG\n+LDVTLFEKK-DLGGVCLNEGCIPTKTLLYSAKVYDYAKHGD-KYGVY-AP\n+---DVTFDFGKIIARKNKTVRKLVAGINATMKAHNIQVV-KGEAHIKGRT\n+E-EAIEI-------H-CN--DETFQAKN--LLLCTGSEAFIPPIPGVEE-\n+--------AGDRVVTNREILAMKEQPSSLVIIGGGVIGMEFASLYNSLGS\n+EVTVIEMLPE-I-LGGLDSEISAMLRDIYTK-KGIRFHLSCKVTEIKDN-\n+----E--V--------I--FMD---SE-GAQGFVTGEKILMSVGR-RAVT\n+TGFG-LETLGVETER-G-A-VKVDT-QMRTNVPNVYAAGDITGFSMLAHT\n+ASREGEVVVNNLT------GL-E-DEMRYHAIPGIVYSNPEVATVGLTEE\n+QARHKSI---EYGVAKLPMTYSGRFVAENEGATGLCKVLFSPQ-QK--IL\n+GVHLLGNPCSEMIHSACMAIE-QG----MTVEALQKVVFPHP-TVSEIFK\n+ETLFTIK-------\n+>742766.HMPREF9455_02296\n+-------------------------MLYDIAIIGGGPAGYTAAERAAANG\n+LKTILFEKN-ALGGVCLNEGCIPTKTLLYSAKTLDNVKNSA-KYGVS-VE\n+-G-QPGFDLSKIIARKQKTVRKLVAGIKQKMTAHEVEII-NAEVHLIEED\n+NSGNIL----------LGNDDETYTAKY--ILLCTGSETIVPPIKGLDT-\n+----------SGYWTSKEALDNKEVPQSLAIIGGGVIGVEFASFFNSLGV\n+KVSVIEMLPE-I-LGAMDKELSAMLRTEYAK-KGIDFYLGTKVVEVK--D\n+--G-Q--V--------I---IE---KD-GEQSSVEAAQILLSTGR-RPVT\n+ANLN-PENLNIEMYR-N-G-VKVDE-FMRTSHPRIYACGDITGYSLLAHT\n+AVREGEVAANHIL------GK-A-DKMSYKAIPGVVYTNPEIAGVGQTEE\n+ELTAKGI---KHTVLKLPMAYSGRFVAENELVNGMCKLIIGED-EK--II\n+GCHMLGNPASELIVIAGIAIE-KE----FTVEEFRKIVFPHP-TVGEIIH\n+ETLFV---------\n+>742767.HMPREF9456_03169\n+------------------------MTLYDVAIIGGGPAGYTAAERASANG\n+LKTVLFERN-ALGGVCLNEGCIPTKTLLYSAKTLDNVKNSA-KYGVG-VE\n+-R-SPTFDLPKIIARKQKTVRKLVAGIKQKMAAHDVTVI-IGEATIEGED\n+GERNILI-------S-CN--SETITAAK--VLLSTGSETIIPPIKGLSE-\n+----------SGYWTSKEALDNKGVPESLAVIGGGVIGIEFASFFNSLGV\n+KVTVIEMLPE-I-LGAMDKELSAMLRAEYTK-KGIDFHLNTKVVEIK---\n+--DGQ--I--------I---IE---KD-GEQSTIEASQILLSTGR-RPVT\n+ANLN-LDKLNIELFR-N-G-VKVNE-NMQTSHPNVYACGDITGYSLLAHT\n+AVREGEVAINHIL------GK-T-DSMSYKAIPGVVYTNPEIAGVGQTEE\n+ELAAKNI---KYTAHKLPMAYSGRFVAENELGNGVCKLIIDED-SK--II\n+GCHMLGNPASELVVIAGIAIE-KG----FTVEEFQKIVFPHP-TVGEIIH\n+ESLFL---------\n+>763034.HMPREF9446_01370\n+------------------------M-RYDIAIIGGGPAGYTAAERAAAGG\n+LQTVLFEKK-AIGGVCLNEGCIPAKTLLYSAKLWDNLKTAS-KYGIS-VP\n+-D-AAAFDMEKIIGRKNKIVKKLTGGVKMTVSSYGAAIV-EQEALIVGEE\n+N-GLFRI-------S-AG--GEMYEATY--LLVCTGSDTVIPPIPGLAE-\n+----------VDYWTSREALESTVLPRSLAIIGGGVIGMEFASFFNSMGV\n+RVSVVEMMPE-I-LGAMDKETAGLLRTEYRK-RGIDFYLDTKVTAVG--K\n+--E-G--V--------T---IG---KD-GKTSLVEADKVLVCVGR-KASL\n+GRVG-LDKLNIELLR-N-G-VKVDE-HLQTSHPRVYACGDITGRSMLAHT\n+AIRESEVAVNHIL------GV-E-DLMDYDCIPGVVYTNPEVAGVGKTEE\n+ELKAAGT---GYHVQKLPMVYSGRFVAENEGVNGLCKLIMDDD-DR--IV\n+GCHILGNPASEIIVIGVLPYS-ADIPWRNSRKVYSRILRPVKFSMKRSFP\n+DVVH----------\n+>471870.BACINT_04803\n+------------------------M-KYDIAIIGGGPAGYTAAERAAANG\n+LQTVLFEKK-AIGGVCLNEGCIPTKTLLYSAKLWDNMKGAS-KYGIS-VP\n+-D-GSAFDMKKIIDRKDKIVKKLTGGVKMTVNSYGAVIV-PQEAIIVGEA\n+D-GRFQL-------S-AA--GEVYEVTY--LLVCTGSDTLIPPIKGLSE-\n+----------IDYWTSKEALEITTLPRSLVIIGGGVIGMEFASFFNSMGV\n+QVHVVEMMPE-I-LGAMDKETSGMLRS'..b'GVIGLELGQVYKRLGA\n+DVSVIEYMDR-I-IPTMDSGLSKELNKVLKK-QKFKINASHKVKSVERVG\n+--D-----E---V--IVK--AD-N-KK-GEEVEFKGDYCLVSVGR-RPYT\n+DGLN-AEAAGVTLND-RGQ-IDVNE-NLQTSAKNIYAIGDVIKGAMLAHK\n+AEEEGVFVAETLA------GQ-KP-HIDYNLIPGVVYTWPEVASVGKTEE\n+QLKEAGV---AYKTGQFPMRALGRSRASMD-LDGFVKVLADKTTDE--VL\n+GVHMVGARAADLIAEAVVAME-YRASAE----DISRMSHAHP-TFAEAIK\n+EAALAATGDRALHV\n+>688270.Celal_3632\n+----------------------M-S-LYDVAIIGSGPGGYVAAIRCAQLG\n+MKTAIIEKYSTLGGTCLNVGCIPSKALLDSSHHYEDAIKHFEEHGIE-IS\n+-G-EIKLNLEKMISRKQSVVDMTTKGIEFLMSKNKIDVF-TGTGSFKDAT\n+HINVAKN-------D-GT--TETIEAKN--TIIATGSKPSTLPFIKLD--\n+---------KERVITSTEALELKEVPKHMIVIGGGVIGLELGQVYKRLGA\n+EVTVVEFMDR-I-IPGMDGALSKELMKVLKK-QKIKFQLSHKVKSVERNG\n+--N-----E---I--IVK--AD-N-KK-GEEITFTGDYCLVAVGR-HAYT\n+DGLN-LEAAGVKLEE-RGR-VAVNG-QLQTNVSNIYAIGDVIKGAMLAHK\n+AEEEGTLVAEVLA------GQ-KP-HIDYNLIPGVVYTWPEVAAVGQTEE\n+QLKEAGI---EYKAGSFPMRALGRSRASGD-TDGFVKILADKKTDE--VL\n+GVHMIGARVADLIAEGVTAME-FRASAE----DIARMSHAHP-TYAEAVK\n+EAALAATEDRALHV\n+>886377.Murru_3269\n+----------------------M-N-QYDVAIIGSGPGGYVAAIRCAQLG\n+MKTAIIEKYAVLGGTCLNVGCIPSKALLDSSHHYEDAVKHFEEHGID-IP\n+-G-EVKVNLKQMIARKQAVVDQTTKGVEFLMSKNKIDVY-HGVGSFKDAT\n+HINIK-K-------D-GK--TETIEAKN--SIIATGSKPSSLPFIEID--\n+---------KERVITSTEALKLKEIPKHLIVIGGGVIGLELGQVYKRLGA\n+EVTVVEFMDR-I-IPGMDGALSKELTKVMKK-QKVKFNLSHKVKSVERKG\n+--D-----E---I--IVK--AD-D-KK-GKEVTIKGDYCLVSVGR-KPYT\n+DGLN-AEAAGVKLDD-KGR-VEVNE-HLQTNVSNIYAIGDVVKGAMLAHK\n+AEEEGTMVAELLA------GQ-KP-HIDYNLIPGVVYTWPEVAAVGKTEE\n+QLKEEGV---AYKSGQFPMRALGRARASMD-IDGFVKILADKNTDE--VL\n+GVHMIGARCADLITEGVTAME-FRASAE----DISRMSHAHP-TFAEAVK\n+EAALAATDDRALHV\n+>313603.FB2170_12491\n+----------------------M-T-QYDVAVIGSGPGGYVAAIRCAQLG\n+MKTAIIEKYSTLGGTCLNVGCIPSKALLDSSHHYEDAVKHFEDHGIE-IP\n+-G-EIKVNLQKMIARKQGVVDMTTKGIQFLMDKNKIDVY-EGLGSFKDAT\n+HINIAKN-------D-GE--TETIEAKK--TIIATGSKPSTLPFITLD--\n+---------KERVITSTEALKLNEIPKHMIVIGGGVIGLELGQVYKRLGA\n+DVSVVEFMDR-I-IPTMDAGLSKELMKSMKK-QKVKFHLSHKVKSVERKG\n+--D-----E---V--IVK--AD-N-KK-GEEVTLKGDYCLVSVGR-RPFT\n+DGLN-AEAAGVKLDD-RGR-VEVNN-HLQTNVPNIFAIGDVVRGAMLAHK\n+AEEEGTMVAEYMA------GQ-KP-HIDYNLIPGVVYTWPEVAAVGKTEE\n+ELKEAGI---NYKTGQFPMRALGRSRASMD-VDGFVKILADATTDE--VL\n+GVHMIGARCADLISEAVTAME-FRASAE----DIARMSHAHP-TYSEAVK\n+EAALAATENRALHI\n+>398720.MED217_06986\n+----------------------M-S-TYDVAVIGSGPGGYVAAIRCAQLG\n+LKTAIIEKYATMGGTCLNVGCIPSKALLDSSHHYEDAVKHFEEHGIE-IP\n+-G-EVKINLEKMMGRKASVVEQTTKGIEFLMSKNKIDTY-QGVGSFKDKT\n+HIHIAVA-------E-GD--DVEIEAKN--TIIATGSKPASLPFIEID--\n+---------KERIITSTEALKLKEIPKHLIVIGGGVIGLELGQVYKRLGA\n+EVTVVEYLDR-I-IPTMDGAQSKELTKVLKK-SKMKINTSHKVSAVERKG\n+--D-----E---V--IVK--AT-D-KK-DKEVEFKGDYVLVSVGR-KAYT\n+DGLN-LDAVGLKTDD-RGR-IEVDE-HLQTAVSNIYAIGDVVRGAMLAHK\n+AEEEGVFVAETLA------GQ-KP-HIDYNLIPGVVYTWPEVASVGKTEE\n+QLKEAGT---AYKSGQFPMRALGRSRASGD-IDGFVKILADKETDE--VL\n+GVHMVGARVADLIAEGVTAME-FRASAE----DIAIMSHAHP-TYAEAVK\n+EAALAATEDRALHI\n+>313590.MED134_14296\n+----------------------M-S-SYDVAVIGSGPGGYVAAIRCAQLG\n+MKTAIIEKYSTLGGTCLNVGCIPSKALLDSSHHYEDAIKHFEEHGIE-VG\n+---DVKFNLEKMIARKQSVVDVTTKGIEFLMGKNEIDVY-QGVGSFKDAT\n+HIDIAGE-------K-----NLTIEAKN--TIIATGSKPSTLPFINID--\n+---------KERIITSTEALKLPEVPKHLVVIGGGVIGLELGQVYKRLGA\n+EVTVVEYMDR-I-IPTMDGAQSKELLKVFKK-QKVKFALSHGVTAVERDG\n+--D-----E---I--TIK--AT-NNKK-GVDVEFKADYVLVAVGR-RAYT\n+DGLN-LDAVGIKTDE-RGK-VEVNE-HLQTNVSNIYAIGDVIKGAMLAHK\n+AEEEGTLVAEILA------GQ-KP-HIDYNLIPGVVYTWPEVASVGKTEE\n+QLKETGV---AYKSGQFPMRALGRSRASGD-TDGFVKILADKETDE--VL\n+GVHMVGARVADLIAEGVTAME-FRASAE----DIARMSHAHP-TYAEAVK\n+EAALAATEDRPIHI\n+>983548.Krodi_2977\n+----------------------M-S-SYDVAVIGSGPGGYVAAIRCAQLG\n+MKTAIIEKYSTLGGTCLNVGCIPSKALLDSSHHYEDAIKHFEDHGID-VG\n+---EVSLNLEKMISRKQGVVDTTTKGIEFLMGKNNIDVY-QGVGSFKDAT\n+HINIAGE-------K-----NETIEAKN--TIIATGSKPSTLPFITLD--\n+---------KERIITSTEALKLPEVPKHLVVIGGGVIGLELGQVYKRLGA\n+EVTVVEYMDR-I-IPTMDSAQSKELLKVFKK-QKMKFALSHGVTAVERNG\n+--D-----E---V--TVK--AT-D-KK-GQEVEFKADYVLVAVGR-HAYT\n+DGLN-LDAVGIKTDE-RGK-VEVNE-HLQTNVSNIYAIGDVIKGAMLAHK\n+AEEEGTLVAEIMA------GQ-KP-HIDYNLIPGVVYTWPEVASVGKTEE\n+QLKEAGV---AYKSGQFPMRALGRSRASGD-TDGFVKILADKTTDE--VL\n+GVHMVGARVADLIAEAVTAME-FRASAE----DIARMSHAHP-TYAEAVK\n+EAALAATEDRALHV\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,4656 @@\n+>376686.Fjoh_1608\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------MEKQ---------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------P----------------------\n+-----------------------N---L---------------NNSLL-Q\n+EWSGPYGGVPDFTKYKISD-----------FKPAIEFAIQEKLEEIDAIA\n+DNSEKPTFENTVQALELSGE------KLDRIHSVYGIYRSNLSTPEFNAV\n+DTEMSPKLAEISDKLYQNEKLFLRIEELYKSEES--KKLTAEQQRLLWLY\n+YTDFVREGAELNKEDKEKVAKINQELAGLFTLFSQKLLAEENDQYLEL--\n+-NSESDLEGLPEEFKNAAIAEAKERN-LNV-LACIGNTRSSIEPFLTFSN\n+RRSLREKAFDIFVKRGDNPN-ENNTNETLVSILRLRAEKAKILGFKNFAE\n+WSLSNKMAKDPQKTLDLMNSVWKPAVEKVKNDVSAMQKMVD---------\n+EE-----GG-DFKIQPWDYRFYAEKVRKAKYDLDQNEIKQYLQLENLR-E\n+GMFWTAG-ELFDLGFKQLFD--VPVYHQDVRVWEVNN-KNTGKVIGLWYF\n+DPYARTGKRSGAWMNSHRDQQ------K--I------KENVLPIVSNNCN\n+FIKGNADESVLISWDDATTLFHEFGHALHGLCSNVTYPSLSGTSVARDYV\n+EFPSQLLEHWLATPEVLN-KFALHYKTNEPLSQSLVERIAKAANFNEGFA\n+TVETISSSFVDMKLHLTT-------------------------EKVD--P\n+HQFEKDIL-AEINM----P-SEIVMR-HRIPQFAHIFSSD-GYAAGYYSY\n+LWADVINADAYEAFLEGN-GPFDKQVAKRLYDIVLTAGNTIDNETMYENF\n+RGH-APKSDALMRARNFPVEN-----------------------\n+>313595.P700755_00882\n+--------------------------------------------------\n+--------MKPLK-------------------------------------\n+-------------------------LTA-IA-LLMTCFACNT--------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------EDKS----------------------\n+-----------------------K---D---N---M--MA---DNTLL-K\n+KWEGPYEGVPDFDAMNLKD-----------LEPAMDAAIEEHLKEIDEIA\n+NVKETATFENTIKAMERSGK------TVDRVYTYYGIWSSNLSSEEFRDI\n+QQKLSPKLSDYQSEIRQNEKLFNRIKSVYESSQK--NPLEPQAQRVVDLV\n+YKSFEMNGANLDDEGKTRYAEINKELAKIYTDFSNNILHDEE-NYVTF--\n+-LNKNQLSGLSDSFIKSAKKTAEEQG-KPD-QYAIVNSRSSMDPFLTYSD\n+ERKLRKQVWENYYSRGDNND-EYDNNALIKEILKLRDERVKLLGYDNFAE\n+WRLQDRMAKNPENAMDLLMAVWPSAIARVEEEVEDMQKVAE---------\n+QE-----GA-DFEIEAWDYRYYAEKVRQEKYDLDSEEVKEYLVLENLT-D\n+AIFYVAG-RLFDFEFSEITDVSVPLFHEDVKVFEVTE-KSNGEHVGVFYL\n+DPYARKGKRSGAWATTYRSYT------N--F------DGETNVLASNNSN\n+FVQAAEGEPILVSWDDAETFFHEFGHALHFLSADVKYPTLNGG--VRDYT\n+EFQSQLLERWIYTDEVIN-NFLKHYKTGKPMPAELIAKIKNASKFNQGFA\n+TTEFLASAIMDMKYHTT----D-------P-------------KTIN--P\n+KTFEKETL-DQLNM----P-DELVMR-HRSPQFGHVFSGE-GYATGYYGY\n+LWADVLTSDAAEAFAEAEGGFYDETLSKNLVDFLFAPRNAIDPAEAYRRF\n+RGR-DAEIDALMRDRGFPVPKK----------------------\n+>983544.Lacal_1935\n+--------------------------------------------------\n+-----MQTKKSIK-------------------------------------\n+-------------------------LIL-LT-VLITITACKK--------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------EEQK----------------------\n+-----------------------K---E---T---V--MA---DNLLL-E\n+EWTGPYQGVPAFDKMKVED-----------VKDAIEKGMALGLEDIEAIA\n+NNPDEPTFKNTIEAMERAGK------PLNRAFTYYGIFSSNMSSPEFREV\n+SSALAPKLSEYRSKINQNEKLFKRIKTVYDASQK--TPLDADQQRVVELV\n+YKGFEMNGAELDTEKKKRYAEINKELSSLYSDFSNNVLHDEE-NYITY--\n+-LTKDQLDGLSDGFIKSAAAIATANG-EDG-KYAITNTRSSMDPFLTYAT\n+NRELRKQVWTNYYSRGDNGD-EYDNNAIIAKILKLRRERVELLGYDNYAD\n+WRLQDRMAKTPENAMNLMMAVWPAAIARVKEEVADMQAVAN---------\n+KN-----GD-NITIEPWDYRFYAEKVRKAKYDLDSDEVKQYLQLDKLT-Q\n+ALFYTAG-RLFNYNFKPITDGSVPVFHEDVKVWEVTD-KDSGEHIGLWYL\n+DPFARQGKRSGAWATTYRSFT------T--F------DGKTNVLASNNSN\n+FVKAAPGEAVLVSWDDAETFFHEFGHALHFFSSNVKYPTLNGG--VRDYT\n+EFQSQLLERWLSTDQVIN-QFLVHNKTGEPMPEELVSKIKKASTFNQGFG\n+TTEYLASALMDMKLHLA----D-------P-------------ENID--I\n+DKFERETL-AELNM----P-KELPMR-HRTPHFGHVFSGE-GYATAYYGY\n+MWADVLTSDASEAFKEAPGGFYDAEVAEKLVKYLFAPRNSMDPAEAYRLF\n+RGR-DAKIEALMKDRGFPITK-----------------------\n+>391603.FBALC1_06208\n+--------------------------------------------------\n+------MISKSIK-------------------------------------\n+-------------------------TAI-LG-SIVLFTSCKE--------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------EPKT----------------------\n+-------------'..b'-SDGAHLGLLYL\n+DFFPRKGKRSGAWMNNLREWT---------P--------TQRPHILLVMN\n+FTPPTAGKEAMLTLSEVHTLLHEFGHSLHGLLTQTRYSSMSGTNVERDFV\n+ELPSQFMENYLLQPDVVTELLSKHYQTGEPLPAKLLNKAIQATQYPVGYS\n+TIRQVIFGKLDMAYHTLA------------------EGES---LPDD--L\n+YTYERETL-RGTTLRDKER-DPEHPKHIIATAFSHIFAG--GYAAGYYGY\n+KWSEMLATDAFERFSEE-G-IFSPTVATDFRHQILERGDELDPMELYVRF\n+RGR-KPTLAAMLKRDGITPQEEVPAN------------------\n+>553175.POREN0001_0430\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MKA--SSTAQ---------------TI---LDQLF-V\n+NPSTPY-GAFPFDRIKDEH-----------FAPTFRAAIAQYRAELAAII\n+ENPDPPTFANTIVALEEMGS------ALDAVEGVFFNLLHANSNAQLMAL\n+AEELSPELTALGNDTSLSPELFERIRIVYEQRES--LNLDEADRRLLENC\n+YDGFTRQGALLPPEKKEILRTLREELSLATLTFGNHVIKEEN-AFSLYI-\n+-DQADAVAPLPQAIREKTASAALEKG-HKG-GYLFDLSFPCYTAIMKFCP\n+DPNIRQQMYLAKATLCCHGG-ETDNRAITQKIVNHRLQIAQLLGYKSYAD\n+YALEKRMLNTPEQVMQLLTDLRESYKPTGVKEMEAIERLK----------\n+----------GAPLEPWDVMYYIEQYREQHYAFSQEELRPYFPLHRVI-E\n+GVFGLAS-RLYDISFIPTKE--LAIYHPDVLPYRVQD-NKTKQLLGLLYL\n+DFFPREGKRSGAWMNNLKEQR---------G--------ERRPHILLVMN\n+FTQATKDLPSLLSPNEVNTFLHEFGHGLHGLLTQSKYTSLSGTNVTRDFV\n+ELPSQLMENWLLQPEFVK-TFALHFQTNQPLPEELLGKMIEAEGYPAGYN\n+TLRQLSFGLLDMAYHTLE------------------A--P---LPEGCDL\n+EQFERDAT-ASVRI----V-PPAPKGCMGSTSFGHLFSG--GYAAGYYGY\n+KWSEVLDADAFSLFQEK-G-IFNPEVAHAFRTHILEKGDLREAMELYVAF\n+RGR-KPEINALLKRDHIL--------------------------\n+>242619.PG1789\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------MNPLL-Q\n+PFDTPF-GSYPFDKISIAD-----------FKEAFAHALAEKRAEADAII\n+NSTEPPTFANTILALELCGE------KLELVCGAFFNLLHADSNDELMNL\n+SREIMPELTRLSTDIALSEPLFVRIRTVWESDEK--EKLSDEEKRLLYNC\n+YRGFVDSGALLPTEKKDRLRTLSEEMSMASLTFGQNVLKDEK-RYKLHL-\n+-SDPAAVAGMPETALALASEKARRKG-YTE-GWLFDLSAPSYFAFMKHCP\n+DGNLRRQMYEAKMCVGFVDN-EYNNEALIRRMVNGRLEEAQLLGYDTFAH\n+FALHDRMAKNPKAVQELLDKLLDAYKPKATDELEMIRKWAADK-------\n+T-----SEVDNFTIQPWDWAYFSEQYKQAHYDLDDEMMRPYFELGRVT-R\n+GIFGLAN-RLYGLHFSERTD--VPVYHPDVKVYEVSD--EDGSYIGLLYT\n+DFFPREGKQNGAWMNNLRDQS---------E--------HQHPHIIIVMN\n+FTPPSADKPSLLTAGEVETFLHEFGHALHGMLSKCRFSSLSGTSVARDFV\n+ELPSQIMENWLTEKDFLD-TFARHYITDEPMPTELVEKLLSARNYLAASG\n+ACRQLSFGYLDMAWHGLS------------------A--P---VDDKLDI\n+KAFEEAAW-SKALI----L-PPSPPNAVMSTAFGHIFSG--GYAAGYYGY\n+KWAEVLDADAFAAFKEV-G-IFDREVAGRFRREILERGDTADAMELYVAF\n+RGH-EPDIAPLLKRTGLV--------------------------\n+>431947.PGN_1776\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------MNPLL-Q\n+PFDTPF-GSYPFDKISIAD-----------FKEAFAHALAEKRAEADTII\n+NSTEPPTFANTILALELCGE------KLELVCGAFFNLLHADSNDELMNL\n+SQEIMPELTRLSTDIALSEPLFVRIRTVWESDEK--EKLSDEEKRLLYNC\n+YRGFVDSGALLPTEKKDRLRTLSEEMSMASLTFGQNVLKDEK-RYKLHL-\n+-SDPAAVVGMPETALALASEKARREG-YTE-GWLFDLSAPSYFAFMKHCP\n+DGNLRRQMYEAKMCVGFVDN-EYNNEALIRRMVNGRLEEAQLLGYDTFAH\n+FALHDRMAKNPKAVQELLDKLLDAYKPKATDELEMIRKWAADK-------\n+T-----SEVDNFTIQPWDWAYFSEQYKQAHYDLDDEMMRPYFELGRVT-R\n+GIFGLAN-RLYGLHFSERTD--VPVYHPDVKVYEVSD--EDGSYIGLLYT\n+DFFPREGKQNGAWMNNLRDQS---------E--------HQHPHIIIVMN\n+FTPPSADKPSLLTAGEVETFLHEFGHALHGMLSKCRFSSLSGTSVARDFV\n+ELPSQIMENWLTEKEFLD-TFAHHYITDEPMPTELVEKLLSARNYLAASG\n+ACRQLSFGYLDMAWHGLS------------------A--P---VDDKLDI\n+KAFEEAAW-SKALI----L-PPSPPNAVMSTAFGHIFSG--GYAAGYYGY\n+KWAEVLDADAFAAFKEV-G-IFDRKVAGRFRREILERGDTADAMELYVAF\n+RGH-EPDIAPLLKRTGLV--------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,5275 @@\n+>694427.Palpr_0832\n+--------------------------------------------M-YLH-\n+LLD-TI---S-KTIKMKL-LKILPFVLLLSPMSLL-AQS-----------\n+--FVYSPD-EVIPVDAK-TIKKTLD-NGFTYYIRQNKAQENKVELRLVIN\n+AGSILETEKQQGLGHFLEHMSFNGTESFPN---AELIKTLEGMGVRFGKD\n+LNAYTSFDETIYYLPIPS--DKVNVGLTVLKDWAM--NLTLSEKEIERER\n+GVVLEEL--RLGKKASTRIR-E-KYLPVLL-AGSLYPLRLPIG-KEEVLK\n+HFTSDELRNYYKKWHRPDLMAIMVIGDINPTEIEKEIIQ-KFGVYKMP-E\n+NS------------------------------------------------\n+---------E--P---R----PVNPVPDH---KE--TKVVVATDPEISGC\n+SVEISYKHKPQKTITQQDYVEHKIYHALYSSMINDRLKELQETETPPFSE\n+AESGYSNYFREVDTYSSYARCAPSKILNAFHSLIVEN-ERVKRYGFTNNE\n+LERAKMKLLSRYERWYNERGKTASDLFADEYQVNYLSG-EPIPGIEYEYE\n+LVKKTLPGIRTTDLNSLVAYYMTDNNRVVVVTGPESASISYPDKKEF---\n+-LTLLAQ----------V-GAEKIKPYREDKVVKELMSSKPKAGTIISER\n+SIPETGLIEWKLSNGATVVFKKT--DFKNNQ--VLFRATSNGGFSNYNAK\n+DDMSALYATKIQDKSGVNGINNTQLKRLMAGKDLSLTQSLVLYNESMSGK\n+YGLKDSEAFFQLLYLYQTAPYFNKNAFKRLMNEEKTEYAKLLDDPSSYFN\n+YQVEQLMNNGNPRRNRWPVKENLDQVDFNRAAAIYKAR----FGSVTGFT\n+YVFVGNVDIDSIKPLVLTYIGGLPGNKKKQGYAEQ-NFTSLLGPATYTFK\n+KGTEDKAEVSIKFVKRAIWDKQKAYAYSAFIELL------KTRLYESLRR\n+EMSGVYGVKVSGKVNQNHEPEASLSLSFGTNTASYEALYKRAILEVKRLM\n+S--DGPTSEELERVKEKMRVTLATDIKENASWLLDIYYAYRYG--DTVMT\n+IEERKQTIEQLNSEKVKEAANEYIDPDKALKFILLPEINTTSSSHLPEQQ\n+KN-----------------------------------------\n+>518766.Rmar_1315\n+------------------------------------------MSV-----\n+--------------------------------------------------\n+---------RIETDTVT-YQKTVLP-CGLRVVTETIPS-VRSVAVGLWVD\n+VGSRDEAEEEAGITHFIEHMVFKGTERRRT---HQIAQRIEYVG---GY-\n+LNAFTTKEHTCYYVRVLD--EYLDRALDTLIDLAF--RPRFPEREIEKEK\n+EVILEEMK-MYEDTPDEYIF-D-LFEELVY-AGHPLGRPI-VG-REETVR\n+SFTRAMLLDFMARHYTPDRMVLAAAGRLRHERVVALTER-LLRG--VA-P\n+RP------------------------------------------------\n+---------T--N---N----RQRQPVPA---YR--P-GERIERRSVQQA\n+HLVLGG---RGYDLHHPRRAALTVLNTLLGGGMSSRLNQNIRERYGYCYN\n+IYSFVNLH-ADVGDWGVYMGTDPR-RVARAEQLIRRELERLVQEPVGRRV\n+LTHAKNQVKGTLML--GQENM---SSRMMRLGRQELYF-GRYYSLDEALQ\n+EADR----VTAEEVQAVARELFAEQPYSKVVLLPE---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>879243.Poras_1460\n+--------------------------------------------------\n+--------------------------------------------------\n+------------MTSPQ-LQYHTTA-QGLRIVYYPIP-S-QVTYIGYMVQ\n+TGSAQDPQPYHGLAHCTEHMLFKGTHKRHA---LHLVNRVEAVG---AD-\n+LNAFTTKEDTTLHITIPS--RYALRAVHLLTDIVL--NSYIPTEELSKEQ\n+EVIIEEIA-SYLDAPSERIY-D-EFEELLF-SGTPLAHN-ILG-SEQSVR\n+RISSTVVRRFMDQYYRPDNMVLGIWGKIDFDKAVEMIEH-LYSE---P-R\n+V-------------------------------------------------\n+------------A---AGDPFKVPKVKPTTTPER--L-IAKTHHYRTNQC\n+HCIIGTH---APSLHNRERYAMTLFNNFIGGPAISSQLNLHLREELGLVY\n+SVEANYTPYLNDGVWNVYLGTGGD-TLQQAVEAVHRILDRYVTTPMSMEQ\n+LAISKQQIVGQLLLA--NDQH---DSELITMLKSYLYF-GRVSSVAEVAE\n+----RIQAITPEEITETVGRYLTRAQRHTLIYK-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>596327.PORUE0001_0121\n+--------------------------------------------------\n+--------------------------------------------------\n+------------MTSPQ-LQYYTTT-QGLRIVYYPIP-S-QVTYIGYMVQ\n+TGSAQDPQPYHGLAHCT'..b'-------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>743722.Sph21_0520\n+-------------------------------------M----------G-\n+S--MLI-G-L-LG-SS--SL------------------------------\n+---------LNAQEKIQ-FKEFKLD-NGLDVIMHQDKT-TPIAAVSVLYH\n+VGSKNEKPDRTGFAHFFEHLLFEGSENIGR---GEFMKKIQGIG---GT-\n+LNAYTSNDQTYYHEVVPS--NYLETALYMESERM--LHAKIDSVGVETQR\n+EVVKEEKRQRMDNQPYGSIL--IEVLKRAY-HKHPYQWAP-IG-SMDHLN\n+AASLQEFMDFYKTYYVPNNAVLSIAGDIDYEQTEKWVRK-YFAE--IPK-\n+GEK-----------------------------------------------\n+-----------E-I-VRP-SI---VEPKR---NQ-E-IRDVVYD-NIQLP\n+AVVEAYN---LPRKDSPDSYALNMLSTYLAGGKSSLLTKEVVDKQQKAVQ\n+IMAMPLD-LEDGGLFLFLGIANMGVSADSLEVAIDAQIEKLRTTGITDKD\n+FAKLRAQTENAVV--SRHASVA---GIAESLAEAKVYY-GDAEEINKELA\n+NYNK----VTKEDIQRVAREYLNKDGRVVLHYLPKKGESK----------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>880070.Cycma_1916\n+-------------------------------------M--KK-HLI--W-\n+L--VCV-F-V-V---Q--TA------------------------------\n+---------VYSQTKID-FREFTLD-NGLEVIMHKDNK-TPIVVTSVMYH\n+VGSKNEDPERTGFAHFFEHLLFEGSENIDR---GQYTDLVEGNG---GA-\n+LNAFTSNDITYYYELMPS--NYLELSLYLESERM--LHAKIDEVGLETQR\n+EVVKEEKRQRYDNQPYGTIL--PETLVRAY-SEHPYQWAP-IG-SLDHLN\n+AASLDEFMQFYKDFYVPNNAILTIAGDIDYEQTEEWVRK-YFSE--IPK-\n+GKN-----------------------------------------------\n+-----------A-I-YRP-EI---VEPKK---DK-E-IRDIIYD-NIQIP\n+AIIQAYN---LPPKNHPDAYAMEMLSTYLTGGKSSLMTKELVDKQQKALV\n+VAAIPLD-LEDGGIFIMYGIANMGIEPEALENEIDVLIKQVQDEGISEKD\n+FQKLQNIIENDLV--SKNSSIE---GIAQNLAEANLFY-GDTDYINRELE\n+VYRK----VSRDDIQRVANKYLTLDGRVVLYYLPKPQETAQNE-------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>388413.ALPR1_19213\n+-------------------------------------M--RK-ITV--L-\n+G--LML-G-L-L---S--FP------------------------------\n+---------SLAQKKIE-FKEFDLD-NGLHVIMHQDQS-TPIVVTSVLYH\n+VGSKNENPERTGFAHFFEHLMFEGSENIER---GEYMNIIQGRG---GT-\n+LNAYTSNDITYYYETLPS--NELELALYMESERM--LHSKVDETGVETQR\n+EVVKEERRQRYENQPYGTIL--PETLKRAY-SKHPYQWAP-IG-SMDHLN\n+AASIEEFQQFYKDFYVPNNATLTIAGDIDYDQTEEWVKK-YFSE--IPK-\n+GEK-----------------------------------------------\n+-----------E-I-YRP-DI---VEPKK---TE-E-IRDIVYD-NIQIP\n+AVIQAYN---LPPENHPDSYALSMLSTYLTGGASSLMTKELVDKQQKALF\n+VQAIPLE-LEDGGIFIMYSIANRGVEPADLESEIDKLIQSVQEEGISDRE\n+FQKLQNIMENNIV--SGVSSMS---GMAEALSQAYVTF-GDTDYVNQVMD\n+AFAQ----VTKADIQRVANEYLNLNGRVVLYYLPKDQEPAQ---------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,73612 @@\n+>313594.PI23P_09695\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----'..b'--DKL-S\n+P-EAKRSIRK-SVAILNKNIPNS-DGNTD----ANN--------------\n+--------------------------------------------------\n+-----------------------------IDSILEV---S-----KSI-L\n+NKAI----------------------------------------------\n+------------------------------------------TE------\n+----------------TAT-AE-----RTVLQKE--LEI-----------\n+--------------------------------------------------\n+-----------------------------------------------Y--\n+--------------------------R-------T----------DLE--\n+-LSQK---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------MRG--------IL-------------------\n+----S--------------------------------DFE-REM------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------AQN---T---------------Y----\n+LDTL--QQE--EA-------------LK---K------------------\n+--------S-T---RLA----GGAVIL-----------------------\n+----------------------------------------------GLII\n+V-------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------IV------------\n+---------F-------TFMI--SKDYW-----K-------V--------\n+-Q-------E----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------Y----RE-------RL------\n+-----------------------ERA------------------------\n+-KKYSESLLKSREQLISTVSHDLRTPLNTISGYSDLIEQ--S---G----\n+---------------L-N-TK--Q----LNY--LKKIKSSSGYVDNLVND\n+LLDYSKLEAGK-IQLDKVPFALFQL----IEETA-VDFEEIQSKK-R--V\n+-LLQL-KIADD--L---KT-PII-NDPFRIRQILTNLIGNAFKFTD-S-G\n+-H-VKVAA-VV-----E-EKN------------KAT----WVRIDVEDTG\n+IGIPVE-K-QESIFQEFTQ--AG-AP--SQ-K--AQ-IGYGLGLTISRKL\n+TELLGGKLSLKS-K-------VGKGSTFTVRVPVEFSKI---EV-V-E--\n+-NN----S----------K-A-----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------F-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------V----S--KP---------------------\n+--------------------------------------KELSILVIDDD-\n+ENMLGL-IS--EVCK--I--N----------Y--I--KTET---LLSF-D\n+DFELS----------------K--I------HQ-FDAVLTDIQMP-TTNG\n+FSVLKTIKSIG--Y-------KN-P-VIAMTGQQ-IGNKTDYLDPGFSDV\n+LQKPFTANSLLHVLRSTEKV------A-L-S------N---AI-------\n+------------------------------------------PASE-SSM\n+-FTLKNISPFLDEPNAIQEVLQVFLENTNKDLAFLLSAVGDKDYTDIRAT\n+SHKMLPMFRQLEIQDA-IHLLEHLENISDDAKGEKT-FNILS-E-LKEVL\n+SNL-ES---EI-Q-N-Y-L-------SKHSIDID---\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,10286 @@\n+>926562.Oweho_2079\n+-------------------MKSKAVSTLECTHCHQPV-V----DQISSDD\n+----------------------G--QKTYCCYGCKVV-DE-LLTEKK---\n+----------SIL-----APE----------------------G------\n+---------LN--HQKYGYLDEPKIKASLLDFDEG-KFVHINM---HLPS\n+IHCSS---------C-IYLLESLPD---VEESIMEVNVHFAKKQASITFK\n+S-DQI-ALSQLAALLDYIGY------------------------------\n+---------------------------TPD--------------------\n+-----------------FQTK-----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------LG-------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------G--------------AK-K-K---QNR\n+---------LLIQLG-VAGFFFGNTM-LL------AF----PE--YFG--\n+-----N------------SLSADKSLQVFFRYLM---MGFSLPVILFSGR\n+DYFINAIK--SLR-AGV------LSIDLPIALGVSVLFLRSAYEVI----\n+----------S--H---TGAGYFDSLTGLIFFLLIGKWYQQKTYE-NFTF\n+DRDLKSFLPLAANLVL---K-D----------------------------\n+-----GT--EKP---ISIDDLSEGDVVLVRQGEVLPADGVLL-----QQD\n+-AQVDYSYITGESIPVQKQ----------------AGETVFAGARISG--\n+--------GAAQFKISTSVNHSYLSSLWSRDSFKDD--A-HKNSRGLTDK\n+ISQYFTPAIILIAIGSAVA-W-SF-V--------------D-ASKAITVF\n+TAVLIVACPCALALAEPFASGSMMRAFGKHGFFLKNSDVINRLQKITHIV\n+FDKTGTLTHQDQIQ--VNWH---------GD-EL-SF-------DEKLAI\n+ASIAKNAQHPLAKPLLTFLNI----------------------------T\n+K-AS--ATHATQFTEATGEGVSAI-I--QND--NYRLGKASFL--K----\n+-L---------------------EER-------AETTSVYVE----K---\n+---NNKALGYFSFFQKAREEAGELAATLKEE-Y-N-ISLLSGDNEA-EKK\n+RFEKIFGSNAELHFNQSPHQKLEHLQQLQKQ-----NAKVLMIGDGLNDA\n+GALQQSDVGISLC-EKNVNFFPASDALLMADSFAHLDKFLALSQQNKKVT\n+YQAFILSLSY-NVIGLSFAIAG------LL-SP--LVCAILMPVSSVTIV\n+VFTTV---ANQMKVRKTLG-------------------------------\n+--------------------------------------------------\n+--------------\n+>755732.Fluta_3131\n+-----------------------MENQTENNTCYHCH-DS--LSPTIFYA\n+----------------------D--DHSFCCNGCKQV-YQ-LLSSHSLGA\n+YY---EQDANAGI-----RPN----------------------K------\n+-------T----AEETFAVLDDLEIRKKYIDFQEG-STVKLTL---HLPQ\n+IHCAS---------C-IYLLEHLHK---LNEGILSSSVHFPKKTATITVT\n+T-ELI-KLSELARLLTKIGY------------------------------\n+---------------------------EPN--------------------\n+-----------------FKAI-----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------DK-------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------S--------------AS-T-F---DKR\n+---------LLLQLG-VAGFAFGSIM-LW------SF----PE--YL-G-\n+------------------IDQTYSGIREFSSYLS---FAVSIPVLLFSAR\n+DYFKSAIA--GMR-LR------NLNLDIPIAIGILALYIRSCVAIF----\n+----------S--Q---EGPGYMDSFAAFIFFLLIGKWFQGKTY-QWLSF\n+ERDFRAYFPVAVIKKT-----S----------------------------\n+-----SD--SVL---CPIDKLQVGDEISIRNEEIIPCDCILL-----TEK\n+-ATVDYSFVSGEADWIEKK----------------KGDLLYAGGKNFG--\n+--------ETIQLVVSKTTERSTLTQLWN-DRHTKR--T-ELSFQTRQDR\n+ISKYFIAAVLILAIVSSIV-W-IW-I---------------DPRQIPEVV\n+TAILIVACPCALALSVPFVYGNMLRVLGKNGFYLRNTAIIERIQQCNYLV\n+FDKTGTLTEQDHKQ--IEY--T-------GR-TL-SE-------FEKLAL\n+HEMTKHAIHPYARAIHDYFSLT----------------------I----Q\n+--QS--D-ATISPIEIPGRGISFG---------FFQLGSASFL--G----\n+-L-------E-E------------Q-------YPNESVVYFA----A---\n+---EGKLLGTFLFHSKLRNQLKELVQNLGST-Y-Q-LAVISGDKPK-DLE\n+LLKQLFPVGTSFHFEQQPLQKKEFIQDLQAK-----GNYTLMIGDGLNDA\n+GALNEAFVGIALS-ENLVRFTPASDAILKAENLNKLAAYFQFIRDGKRFL\n+RICFAFSLCY-NLTGIGFAVTG------QL-TP--FVATILMPLSSITVV\n+SLATFL----TIRRKFNDV-------------------------------\n+--------------------------------------------------\n+--------------\n+>649349.Lbys_2752\n+----------------------MKIKEIEQVKCYHCD-SL--CEQETLHY\n+----------------------D--DKVFCCVGCKTV-YE-ILSDNGLCT\n+YY---DFNDGTNL-----KAK----------------------N------\n+---------F--Q-GKYDFLSNETICSSLLDYNSQ-NLAKVTL---FIPD\n+VHCSS---------C-VWLLENFQK---IKEGILTSRLN'..b'TGDNQQV-AE\n+AVAKQIG-VTEAWGNLMPEDKVEAVKKLDKS-----EKMVAMVGDGVNDA\n+PAMAKSTVGIAMGAAGSDVALETADIALMGDRLESLPFAIGLSRKARGII\n+KQNLWISLGV-VAALIPLTILG------I-ASI--GPAVIAHEGSTLLVV\n+FNALRLLAYDNDQKKQAPKPKEKKHA------------------------\n+--------------------------------------------------\n+--------------\n+>714943.Mucpa_1948\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---MA---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------PKKNS--DNNM--\n+K-QEHQARDKK------------QPGI-------------DISSA-----\n+KHKE-EKHNHD--ENA--AGH--N--H------E-HG-GI-F-G---QNT\n+--------E-LIFAA-LSGVFLAVGF-G----------------------\n+------LS-FV-H-ALP-------------VLTS---TILYGIGYFFGGF\n+YTTKEAYQ-A-IS-KG------HFEIDFLMLVAAVGAGFLG---------\n+---------------------QWAEGALLLFLFSFGHSLEHYAMGKATKS\n+IAALADLAPKTAILRR--D--------G--------K-------------\n+---------ETE---LSIEELVLGDVIIVKPNSKISADGAVI-K----GE\n+-SSVNQAPITGESIPVDKSPVADPDN-YTDDKILKPENKVFAGTINGS--\n+--------QVLEVKVTKLAADSTLSRLVKLVNDTE--A-QKSPTQLFTDK\n+LQKFYVPAVLLLVVTLLFA-Y-LV-I-D-----------EP-FSKSFYRA\n+MAVLVAASPCALAISTPSAVLSAIARAARGGVLIKGGGPLEELGALTAIA\n+FDKTGTLTEGKPKLTGVVA--L--------A-QL-SE------NEVLEMA\n+IAVEKLSDHPLAAAIVKGGLER-L-Q------------------QKNI--\n+------P-SAQNLEAVTGHGVKAT-V--GGK--KVVIGNRSLF-K-E-L-\n+--A------T-E-VNEQVEKLE--K--------EGNTTMLVE----L---\n+---DGAIVGLVSLMDVPRKEAKNTLAELKELGI-KKMIMLTGDNQQV-AD\n+AIAKEIG-ITNAMGGLLPEQKVQAIQNLIKT-----EKKVAMIGDGVNDA\n+PAMAKSTVGIAMGAAGSDVALETADIALMADRLDNLPFAIGLSRQSRRII\n+KQNLFISLGM-VAILIPLTILG------I-SGI--GPAVVGHEGSTLVVV\n+FNGLRLLVYQNNRK------------------------------------\n+--------------------------------------------------\n+--------------\n+>714943.Mucpa_3329\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------MKK--\n+Q-TPAKAADKK------------QPRV-------------DISTA-----\n+RDKE-EKHDLH--ENE--PGH--D--H------E-HG-DL-F-G---KNT\n+--------E-LIFAI-LSGVFLALGF-G----------------------\n+------LS-FI-H-SLP-------------PLTS---TIVFGIGYFFGGF\n+FTTKEAYE-A-VS-KG------QFEIDFLMLVAAVGAAFLG---------\n+---------------------EWAEGTLLLFLFSFGHSLEHYAMGKATRS\n+IAALADFAPKTAIVRR--D--------G--------K-------------\n+---------ETE---VPIEELVIGDIIIIKPNSKISADGAII-K----GE\n+-SSVNQAPITGESVPVDKSPVADPDK-EHDDKTLKAENKVFAGTINGS--\n+--------QVLEVKVTKLAADSTLSRLVKLVNDTE--A-QKSPTQLFTDK\n+LQMIYVPVVLILVVLLLFA-Y-LV-I-D-----------EP-FSKSFYRA\n+MAVLVAASPCALAISTPSAVLSAIARAARGGVLIKGGGPLEELGGLTAIA\n+FDKTGTLTEGKPALTGVVA--L--------A-KF-SE------DEVLEIA\n+IAVEKLSDHPLAAAIVKGGLER-L-K------------------QKDI--\n+------P-SAKNLQAVTGHGVKAT-V--GSK--KVVIGNRSLF-D-K-L-\n+--S------E-D-IHARVEKLE--K--------GGNTTMLVE----Q---\n+---EGEMIGLISLMDVPRKEAKRTLKELKDLGI-KRMIMLTGDNQQV-AE\n+AVAKQIG-ITDAMGGLLPEHKVKAVQDLIKK-----EKKVAMIGDGVNDA\n+PAMAKSTVGIAMGAAGSDVALETADIALMADRLDHLPFAIGLSRQSRRII\n+RQNLVISLGM-VAVLIPLTILG------I-SGI--GPAVIGHEGSTLVVV\n+FNGLRLLIYQNNRK------------------------------------\n+--------------------------------------------------\n+--------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1246 @@\n+>518766.Rmar_0950\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------MSIVL\n+AFSGGLDTSFCVPYLRETYGEPVYTVTVNTGGLTEAAIAEIEALSQKLGA\n+AGHFTIDGRHDLFRDHLSYLIKGNVLRGGVYPLCVGPERIVQARKVVEVA\n+RQLGARAIAHGSTGAGNDQVRFDVALRILADDLEILTPIRELGLSREAAT\n+AYLKERGI-EVPEKKTAYSINRGLWGTTIGGRETHTTTEPLPDDAYPDTV\n+PPAQA-PDTPL-ELTIAFEQGIPTALDG-----E-AMDPVTLIERLNQLG\n+AAHGVGRGIHVGDTILGIKGRVGFEAPAALILITAHRELEKIVLTRWQRY\n+QKDHLADFYGMLLHEGQYFDPVMRDIEAFLDSSQQTVTGTVRVRLFKGHI\n+DVLGCDSPYSLFN---SKIATYGEQNRLWDGRDAQGFTRIYGVQALLAAR\n+ARQSASSYETNQTAA-----\n+>309807.SRU_2214\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------------MAIVL\n+AFSGGLDTSFCVPYLQATHDAPVHTVTVDTGGLTDDDRTAIEARARHLGA\n+DRHHLIDGRAPLYEDHLSYLIKGNVLKGGVYPLCVGPERIVQARAVAEVA\n+QAVGASTVAHGSTGAGNDQVRFDVALQLVGDDLDVIAPIRELGLSRDAST\n+AYLEARGF-SVPDDTTDYSINRGLWGTTIGGKETLTAKASLPTDAYPDTT\n+APADA-PDAPR-TLTITFANGLPVAVDD-----A-SLSGVEVVETLNEVG\n+GRHGVGRDVHVGDTILGIKGRIGVEAPAAQILITTHRELEKVVLSEQQQV\n+QKHTLGDVYGRLLHEGQYFDPVMRDVEAFLDHSQDVVAGTVTVKLFKGRA\n+TVQGVDSPHSLFD---AGTATYGEENALWDGRDAEGYTTLAAIPSLLAKK\n+ARADTDPPGSEPMIAESTTG\n+>595499.SMDSEM_117\n+MNLTVRRANYDDKKYADIICKQIEYSAKVRGTGISRRDPEYIKKKMVDGF\n+SVIAFFNGNLAGFSYFEVFEKKKFLSNSGLIVFTKYRLHGLAKMMKLKIF\n+KLSKKKFPKSKIFSITTSPAVIKINTDLGFKPVLFSELTKSETFWKGCKS\n+CTNYEILLRKKKKMCFCTGLLYDPKY---------KKKKKDLYKGEKILL\n+AYSGGLDTSYCLKYLTNK-GYKVITIIINTGGFKNKELELIEKRALKIGA\n+IYHYSINAKEYYYYKCIKYLIYGNILKNNTYPLSVSSERFFQAILIAEFS\n+KKLNVKAISHGSTGAGNDQVRFDLAFKILCPETVIITPIREKKLSRKEEV\n+DFLESKGL-TISWKKAKYSINKGIWGTSIGGEETLNSSTSLPEEAYPSKL\n+SE--K--K-KK-FLELEFKKGELISIN------KIKDLKLNNILKIEKIS\n+SKFAIGRDCHVGDTILGIKGRVGFEASAALLIIKAHQLLEKHILTKWQIY\n+WKDQLSNWYGNLLHEAQYLDPIMRDIECFFKNSQKRVSGKVKILLNPYRL\n+ELIGIESEFDMMK---SKMAKYGEMNNDWTSDEVKGFIKIFGNQMKIYHN\n+IKKE----------------\n+>641892.DMIN_01050\n+MKITVRIANSDDKKYASIICKEIESSAKVRGTGISKRDPEYIKKKMGDGF\n+SVIAFFNGDLAGFSYFEVFENKNFLSNSGLIVFPKYRLHGLAKMIKLEIF\n+KLSKTKFPNSKIFSITTSPAVIKINTDLGFNPVLFSDLTKSKQFWKGCKS\n+CTNYDILIRKKKKMCLCTGLLYDPKK---------KRNLNNLNKGDKILL\n+AYSGGLDTSYCLKYLTNE-GYKVITIIINTGVFNNKDLESIEKRALNIGA\n+ISHYSINAKEYFYYKCIKYLVYGNILKNNTYPLSVSSERFFQAILIAEFA\n+KNLKVKAISHGSTGAGNDQVRFDLAFKILCPDKIIVTPIRDMKLSRKEEV\n+FFLKSKGV-KISWKKAKYSINKGIWGTSIGGEETLKSSTSLPEKAYPTKL\n+SE--Y--Y-KK-IIELKFKKGELFSVN------NIKDLQINNIIKLEKIS\n+SKFAIGRDLHVGDTILGIKGRVGFEASAALLIIKAHKLLEKHILTKWQIY\n+CKEQLSTWYGNLLHEAQYLDPIMRDIECFFKNTQKRVSGKVKILLNPYRF\n+ELIGIESNFDMMK---SKIAKYGEINNEWTSDEVKGFIKIFGNQMKIYHN\n+IKKYD---------------\n+>706194.SMCARI_129\n+MKITVRIANIDDKKYASIICKEIEDSAKVRGTGISKRDPEYIKKKMVDGF\n+SVIAFFNGNLAGFSYFEIFEKKKFLSNSGLIVFPKYRLHGLAKMIKLEIF\n+KLSKKKFPKSKIFSITTSPAVIKINTDLGFNPVLFSNLTKSKKFWKGCKS\n+CTNYDILIRNKKKMCLCTGLLYDKKNF--------NLKKNYLYKGDKILL\n+AYSGGLDTSFCLKYLINE-GYKVITIIINTGGFNNKDLESIEKKAINIGA\n+LYHYSINAKEYFYYKCIKYLVYGNILKNNTYPLSVSSERFFQAILIAEYA\n+KKLKVKAISHGSTGAGNDQVRFDLAFQILCPDKMIVTPIRDMKLSRKEEV\n+NFLKSKGI-KISWKKAKYSINKGIWGTSIGGEETLKSSTSLPEKAYPTKL\n+SE--Y--Y-KI-YIELEFKKGELLYIN------NIKDLQINNIIKLEKLS\n+SKFAIGRDIHVGDTILGIKGRVGFEASAALLIIKAHQLLEKHILTKWQIY\n+WKEQLSNWYGNLLHEAQYLDPIMRDIECFFTNTQKRVSGKVKILLNPYIF\n+KLIGIKSKFDMMK---SNIAKYGEINNEWTSDDVKGFIKIFGNQMKIYHN\n+IYD-----------------\n+>1074889.MADAR_302\n+MKIKVRISNEEDTKYASLICKKIKESAKSRGTGISKKDPEYIKSKMINGN\n+AVVAFYNGKIAGFSYLEVFQSKEFVVNSGLIVFPEFRKRGLAKIIKIEIF\n+KLSKKKFPNSKIFSITTSNSVIKMNTELGFKPVSFSELTQSEEFWMGCRS\n+CDNFDILTRNKRKMCLCTGLLYNPKEKKK----------KSLTYGDKIVL\n+AYSGGLDTSYCLKYLIQQKGYEVHTVIVHTGGFKDKELKKIEELALNIGA\n+KSHKTIDALEEYYQNCIKYLIFGNILKNNTYPLSVSSERIFQAIKIAQYA\n+NRIKAIAIAHGSTGAGNDQIRFDVAFQIICPEKITLSPIRDLKISRKEEI\n+EYLQNSGI-SIVWDQYQYSINKGIWGTSIGGKETLNSSQKVPDEAYTKKL\n+IR--K--E-SE-NLELEFEKGELVSVN------KKKGKAIKNIIKIERIA\n+SKFSIGRGIHIGDTILGIKGRVAFEASAAIIIIQAHHFLEKHILTKWQLY\n+WKEQLSNWYGMLLHEAQYLDPVMRDIERFLISTQERITGTVYMILYPYRF\n+RLVGIKSKFDLM-ETNIHMAQYGEMNYAWTSEDVKGFTKILSNQMKMYHN\n+LNKKK---'..b'--------\n+>485917.Phep_4209\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------MKKKVVL\n+AFSGGLDTSFCCIYLAQDRGLEVHSVIVNTGGFSDEELKEIEKRAYALGV\n+ASHAVVDETENYYNSCIRYLVFGNVLKNATYPLSVSAERVSQATAIANYV\n+KKIGADYVAHGSTGAGNDQVRFDMIFNIIIPEVEIITPIRDLKLSREAEI\n+EYLNAHGV-EYSAEKARYSINKGLWGTSVGGKETLTSNETLPEEAWPTQV\n+SE--S--K-AR-KLELSFEKGELVAIDG-----ERFE-PVRAIQKLQAIA\n+QPYGIGRDIHVGDTIIGIKGRVGFEAAAPVLIIKAHHTLEKHTLTKWQLS\n+WKEQLSSFYGNWLHEGQFHDPIMRNIEAFLTDTQKVVSGKVFVELLPYRF\n+NIIGIESEHDLMS---NKFGSYGEMNNTWSGEDVKGFSKIFGNQVMIWHK\n+VNSHEG--------------\n+>269798.CHU_3080\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------MKKKVVL\n+AFSGGLDTTYCAKYLSEDLGYELHTAIVNTGGFSKEELADIEKKAYELGV\n+TSHTTLDIIEKYYAECVKYMVYGNILRNNTYPLSVSAERVFQAMAIAEHA\n+KKVGATAVAHGSTGAGNDQVRFDVVFMIMNPGIEIITPIRDMKLSREAEI\n+EYLKKKGV-VRDWSKAAYSINVGIWGTSVGGKETLTSDKTLPESAFPTQV\n+TK--T--G-EE-EVELEFEKGQLVGLNG-----KR-MKSTDAIVELNKIV\n+APYGIGRDIHVGDTIIGIKGRVGFEAAAPMVIIKAHHTLEKHTLTKWQMY\n+WKEQLANWYGNFVHEGQFLEPVMRNIETFLEDTQVHVTGKVKVFAAPYRF\n+HVVGIESAHDLMS---AKFGKYGEENNAWSGDDVKGFSKIFGNQTMIYHR\n+VNEDVKG-------------\n+>649349.Lbys_2279\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------MKKVVL\n+AFSGGLDTSFCVKYLKDDKGMEVHSVLVDTGGFTDEEVADIEKKAYDLGV\n+KTHYTARVADKYYKDCIRFLIFGNVLKNNTYPLSVSAERIFQAVAVAEYA\n+KSIGATAIAHGSTGAGNDQVRFDMAFRIIVPDAEIITPIRDLKLSREAEI\n+EYLKGKGV-QREWHKSTYSINQGLWGTSVGGKETLNSWDYLPEEAYPTQL\n+TK--K--K-PS-EITLEFVKGELKAVNN-----RRFKNPVEAIRRVHALA\n+APYAIGRDTHVGDTIIGIKGRVGFEAPAPLIIIKSHHLLEKHVLTKWQQY\n+WKQNLAEWYGMLLHEGHFNEPVLRDIEAYFEHSQKTVTGTVRVRLAPYNF\n+QVLGIQSDYDLMS---DVFGSYGEMNNAWSGDDVRGFSKIASNQVMIHQK\n+IQELAEKKK-----------\n+>504472.Slin_0407\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------MSQKVVL\n+AFSGGLDTSFCVKYLSEDRGMDVYSVLVDTGGFSDAELKAIEERAYSLGV\n+KSHVTISKTDDYYQQCLKFLVFGNVLKNNTYPLSVSAERIFQAIAAAEYA\n+REIGASAIAHGSTGAGNDQVRFDMAFRIIAPEAEIITPIRDLRLSREAEI\n+EYLKAKGV-DQEWHKAAYSINKGLWGTSVGGKETLTSDQFLPESAWPTQV\n+TK--S--E-PE-TITVTFQHGEIKGISG-AFGDETYNNPVDAIRKLTELA\n+GPFGIGRDIHVGDTIIGIKGRVGFEAPAPLIIIKAHHTLEKHVLGKWQLY\n+WKEQLANWYGTMLHEGQFMDPVMRNIETFLADSQAHVSGKVHVLLAPYRF\n+QVMGIESDHDLMS---SKFGSYGEMNNAWTGDDVRGFSKVASNQVMIYEK\n+INNQ----------------\n+>761193.Runsl_0185\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------MSESKKVVL\n+AFSGGLDTSFCVKYLSEDKGYEIYSVLVDTGGFSDEELKAIEARAYSLGV\n+KKHATISKTQDYYQQCIKYLVFGNILKNNTYPLSVSAERIFQAIAAAEYA\n+KEIGAQAIAHGSTGAGNDQVRFDMAFRIIMPEAEIITPIRDLRLSREAEI\n+EYLKSKGV-DQEWHKAAYSINKGLWGTSVGGKETLTSDKYLPESAFPTQV\n+SK--N--E-AE-RVTLQFEKGELVGIND-----TAY-SPVEAIQKLAEIA\n+APFGIGRDIHVGDTIIGIKGRVGFEAAAPLVIIKAHHTLEKHVLSEQQLY\n+WKEQLSNWYGSLLHKGQFMEPVMRNIETFLADTQQHVTGKVHITLAPYRF\n+YVEGVESSYDLMS---PVFGSYGEMNNAWTGDDVRGFAKVASNQVMIYQK\n+ISELNQ--------------\n+>471854.Dfer_4424\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------MSQPKVVL\n+AFSGGLDTSFCVKYLAEDRGYEVYSVLVDTGGFSDEELKTIEANAYALGV\n+KQHATISKTKEYYNDCIKYLIFGNILKNNTYPLSVSAERIFQAVAVAEYA\n+KEIGASAIAHGSTGAGNDQVRFDMAFRIIVPDAEIITPIRDLKLSREAEI\n+EYLTAKGV-ARDWTKAAYSINKGLWGTSVGGKETLTSDQYLPESAWPTQI\n+TK--T--E-PE-RVTLEFAGGELKGVAG-----EAFENSVTAIQKLAEIA\n+QPFGIGRDIHVGDTIIGIKGRVGFEAAAPLIIIKAHHTLEKHVLTEQQLY\n+WKEQLANWYGSLLHKGQFVEPVMRNIETFLGDTQSHVTGKVHIYLAPHRF\n+HVEGIESAFDLMS---SKFGSYGEMNNAWTGDDVRGFSKVASNQVMIYGK\n+VSDSVN--Q-----------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1888 @@\n+>411154.GFO_0031\n+-MK-----------------------------------------------\n+------F-----PFLRT-------------SI-LILCLA-F-C---LPV-\n+-----L-------AQRNLIELQKDWKFAKGEI------------------\n+---------------------------------------------P----\n+-----TAAETNFNDSNWQDVRIPHDWAISENFIKDGD-------------\n+-----GSTGKLQWKGQGWYRKKLDIAPSF-KDKRVYLIFDGVMAFPEVYI\n+NGKLAGKWDYGYNSFYVDITDHLNF--NGENFLAVHADTRKH-DSRWYPG\n+AGMYRKVQMLVTNPVHVDIWGTYVTTPVIK-KDSASIRISNKIINTT-EK\n+-ADS----------------VKIYQSIL------NPEGNEVSKDSVT-R-\n+-------FIAAG-G-ESFLEINTKVSKPQLWDV---NQPNLYKTITKVF-\n+-V-GGKQTDEKETTFGIRTIKFTADDGFHLNGKRVQLKGVNLHHGHGPLG\n+GAFYPRAAERQLEIMQSLGVNAIRNSHNVAAPELLELCDKMGILFFNEIF\n+DKYDAKAGIVD-TTNFEDFAHRNIKNFVLRDRNHPSVFMWSVGNEIGDVQ\n+WNQNNGFQ--------------------------------RLHTMLNYVN\n+KYDPTRPTTLVNDQL---------------KS-AELRHFD--LYDVHSWN\n+Y--------------------GRRYR--IARKLEPNK-AVVISESASTLS\n+TRGFYEFPLPEKKT-----------DFT-KSLQVSSYDLNA-PDWAEIAD\n+DDFMWQQQEPYIAGEFVWTGFDYLGEPTPYTNKEVTEMGMTDL-------\n+----------EASRSSYFGIVDLVGIPKDRYYLYKSYWKPDETTVHILPH\n+WNWEGREGETTPVFVY-TNGDCAELFINGKSFGKKCKKLD----------\n+-----SETSTDRFRLMWKDVTYEPGEVKAVAY-KDGKKIGENNIKTAGKT\n+SKISLTADR-------------------TSIKAD--GKDLSYILVEAFDK\n+DGNPSPLADNELKIEVSGAGHLAGAGNGDPQSFEPFQN------NKVNLF\n+YGKAMIIVGSDF-EKGKLKLSVK-PENIQK-ESITINVE-----------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------\n+>376686.Fjoh_4074\n+-M--IK----------------------------HK--NIF---------\n+------Q------KIT--I---------------ALLF----S-VS-IF-\n+--AQKQ--------ARIVEDFNKNWNFKLGDY------------------\n+--------------------------------------------------\n+---P-EAINANFTASDWRTLQLPHDWSIEGAFDKDAK-------------\n+---T-KQAQGFLPAGKGWYRKVFTVPANW-KNKTISIEFDGVFKNSEVFI\n+NGKSLGVRPNGYISFGYDLTQYLN-FG-KSNTIAVKVDNDAQPNSRWYTG\n+SGIYRNVRLVASEKLHVGKWGTFVTTPEVS-AEKSKIHLEVTIDNDN-AS\n+-AKE----------------FKLVTSII------NAENKEVVNFTST-E-\n+-------KIGAK-T-SEKKIHDLVLNQPKLWST---ENPYLYKVITKVY-\n+-E-KSKLVDNYETPLGFRYFNFDSEKGFSLNGVPTKIYGVCLHHDNGALG\n+AVENIHAVRRKLALMKEMGANAIRMSHNPHSLEMMQLCDEMGFIVQDEAF\n+DVWKKKKVTNDYHKDWDAWHKQDLEDFIKRDRNHPSVMMWSIGNEIRE-Q\n+FD-ST--------------------------------GIAITRELAKIVK\n+SLDKTRPVTSALTEN---------------VI-EKNFIYQSGALDLLGFN\n+Y-K------------------HEDYK--DFPTKFKGQ-KILASESVSALE\n+TRGHYDF-PDGIKAWPTKHGAPF--DGN-ADWTVSAYDQVK-SYWGATHE\n+ENWKTIKSQDFMAGTFIWTGFDYIGEPDPYP-------------------\n+----------FPARSSYFGIVDLAGLPKDVYYMYQSEW-SNKTVLHILPH\n+WNW--KKDQEVEVWAYYNNADEVELFLNGKSLGKKAK-------------\n+--------QNDDLHISW-RVKFEPGTLKAVSR-KYGKVVLEKEIKTAGEA\n+SKIDLKA---DK-TSIK---------------ND--TYDLVYVTVSMTDK\n+DGNLVPNAMDLVNFEVSGGGKLVGVDNGYQANLDSFKA------NSCKLF\n+NGKCVAIIQSNG-KKENIQLKAMAGNGIPF-SAIQINVN-----------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------\n+>485917.Phep_2757\n+-M--M-----------------------------------L---------\n+------R------KNLVLL------------L-LMLTV----G-AV-AY-\n+----GT--------PRIRQNFNQDWKFFLGDD------------------\n+--------------------------------------------------\n+---A-AAKLPGFKDGKWRTLTLPHDWSIEGKFDEKNP-------------\n+---A-KPEGGGLPTGIAWYRKTFTLPASM-QKKDVFIEFDGVYKNSEVWI\n+NGHLLGKRPYGYISFRYELTKYLK-TG--QNVIAVRVDNAAQPDSRWYSG\n+SGIYRNVWLTATGKVAVNQWGTFVSTPSVS-KTSANVYIKTQIRNKE-RV\n+-KAK----------------IDVKWEVH------DADGKVVSATEMK-D-\n+-------ISLKD-T-LFEVAEFARVNNPKLWSV---KQPYLYKVMTRVF-\n+-V-NKTLTDTYETPLGIRYFNFDAKKGFFLNGESLKILGVCMHHDLGALG\n+AAVNVRAMERQLEILKEMGCNAIRTAHNPPAPELLDLCDKMGFLVMDEAF\n+DIWAKKKNKQDYHLDFPEWHQRDLQDMVKRDRNHPSIILWSIGNEIRE-Q\n+FD-ST--------------------------------GVALTRSLVKMVK\n+DVDATRPVLSALTET---------------D'..b'---------------QNPID--EFHQKHPEWYSPVGSEETSGCG\n+TRNVYYTDSLRGWM-----------A----PINRTAQDDNH---IINPMA\n+RGWQFYHDRPWLAGLFYWTGLDYRGEPNPML-------------------\n+----------YPATGSQFGIFDYCGFPKDEAFYLKSWW-TDEPVLHLSPH\n+WNLSGHEGDSINVWAY-SNCDEVELFVNGKSLGRKSM-------------\n+---------PVNGYIEWK-TIYRPGSLLAKGY-KAGKKVMVEKIETTGKA\n+TRISIEP---YN-TTLK---------------AG--GQDIAIIDLTLKDE\n+KNREVPDAMNEMIVTLTGPATILGYGNGDPGFKEIERPVNGETSFRIKAF\n+SGKAQVIIRSQEGKKGNVQLEVS-GTGLKK-ATQQFIID-----------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------\n+>714943.Mucpa_1754\n+-MIKK----------------------------------LY---------\n+------------FRAII-C------------L-SILPLA-V-S---GQT-\n+----QN--------RRTHVNFDAGWKFSLGNASDPKRDFNYGIG------\n+---------------------------------------NI--FS--KSG\n+ETAG-TCIATDFKDSTWTNVKLPHDWVVALPFQYVKN---------DDID\n+SHGYKPVGALFPENSIGWYRKTFTVNKAD-SGKRYEIQFDGVYRDSKVWL\n+NGYYIGGHFSGYNSFSFDITDFIK-FG-QKNVMVVRADATQS-EGWFYEG\n+AGIYRHAWLNSYNNVHFKTAGGLFAHAEVS-DGKAQVTIEADIENRG-IT\n+-ATE----------------ATLYSYIT------DRNGKIIATGKQL-PF\n+--------TEAI-RENKKLTDEMTIINPRLWSL---DDAYLYRAVSLIK-\n+-SG-GHTIDSVNVKFGVRTFKFDSEKGFFLNGKPLKVQGVSCHQDHAGVG\n+SALPDELQYYRITLLKEMGVNAYRTTHNPPTPELLDACDSLGMLVMDET-\n+---RLLTSGQEYEQQYR--------DLILRDRNHASIFMWSIGNEEYATH\n+RT-DIGKR--------------------------------IAQNQILLQQ\n+QLDPTRTSTYAANMG------------------NVYRGVN-EVIPVRGFN\n+Y-N------------------LSGID--GYHKEHPLQ-PIIGTEVASTVT\n+TRSIYVKDTVHAYV-----------P----D-----YDVTF-PPWASTAE\n+TWWKITDARPWFMGGFAWTGFDYRGEPTPYR-------------------\n+----------WPNINSHFGIMDMCGFPKSVYYYYQSWW-TDKDILHIAPH\n+WNWKGKEGQPIEVWVN-TNADDVELYLNGKSLGKKEM-------------\n+---------TRDGHLVWT-VTYQPGKLVAVAH-KKGKVIAAK-VETTTAA\n+YRIVLSP---SK-KILL---------------AN--GEDAVVVNATVVDK\n+SGREVPDALDLLHFDIKGDAEIIGVGNGDPSSHEPDKCSTGQ--WQRSLF\n+GGKAQLIVRAG-THEGNVAIVAT-GTGLKS-IELPLVQ-K----------\n+-----L--------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------K\n+>760192.Halhy_4898\n+-MQA------------------------------------F---------\n+------------KYLWL-C------------L-LCAAAL-H-A---SAQ-\n+----SS--------PRERINFDANWKFHFGHAANPEKDFNYSLA------\n+---------------------------------------TI--FS--KSG\n+GAAQ-TAIDPRFKDSTWRSLNLPHDWAVELPFAYKDN---------FDVM\n+AHGYKPVGGHFPETSIGWYRKHFRVSPAD-SSQRFQIQFDGVFRNAQVWI\n+NGFYLGTNASGYIGMAYDITDFIN-YN-RDNVIVVRVDATQY-EGWFYEG\n+AGIYRHVWLNKYQNTHIATDGIFAYT-NFQ-GTTTTVQIESTLANEN-TQ\n+-TSI----------------CTLKTYLQ------DRAGKLVGVPKEQ-TI\n+--------TLGA-NTEQTLKHSIPVSKPHLWSL---EDPYLHRLVVEVR-\n+-SN-GKLLDKQSIRYGIRKIEIKPD-GVFLNGEAIKLYGVNCHQDHAGVG\n+SALPDHLQYYRIALLKNMGTNAYRSSHNAPTPELLDACDSLGMLVMDEQ-\n+---RLLNSGPEYMGQFE--------RLVKRDRNHASVFMWSIGNEEGWIH\n+TT-SHGKR--------------------------------IAQTYIAKLK\n+QLDPTRTCTYAADLA------------------NVYKGIN-EVIPVRSFN\n+Y-R------------------QYAVA--DYHAEHPNQ-PIIGTEMGSTVS\n+TRGQYSKDSIRAYL-----------P----D-----QDIHA-PWWASRAE\n+EWWMLAAESDFWLGGFIWTGFDYRGEPTPYQ-------------------\n+----------WPNISSHFGVMDMCGFPKNLYYYYQSWW-TDKDVLHISPH\n+WNWRDKRGQPIDVWVN-SNADDVELFLNGKSLGKQEM-------------\n+---------KRHGHLQWT-VNYEPGKLEAIAY-KKGKKLTAK-VETTGTP\n+TEVVLTP---YK-TTML---------------AD--GQDVSVINVTVVDR\n+EGREVPDADNLIRFAIEGEGKIIGVGNGDPSSHEPDQCVDGA--WQRRLF\n+NGKAQFIVQGS-VKPDIIKIEAT-ASGLWK-GSTDIITVTPREVASVTID\n+KTYELKGEAAKSRPVGQMLGADISFLPELEARGIKFSEKGTPVDAIESLK\n+QHGFNYVRLRIFNNPARDSGYSPQKGFCDLAHTKAMAKRVKAAGMKLLLD\n+FHYSDYWADPGKQYKPAAWRGLGFTELKKAMYDYTRQVIQELKDQGTTPD\n+MVQIGNEINHGIIWPEGKVSNLDQLAQLLNAGTAAVKAVDPNIVMMLHVA\n+LGGQNHESVFFIDNMLARGVHFDVIGESYYPKWHGTLEDLEHNLNDLVRR\n+YQRDVIVVEYSQLKREVNKIAFELPNGKGKGTCIWEPLNTWEQVFDREGK\n+SNELLPVYDEIAKAYLNSNK\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,756 @@\n+>242619.PG0618\n+---------------------------------------------M-T-P\n+ILNTVFPEFKLNAYHN---GE--FKVITNEDL---KGKWSLVVFYPGDFT\n+FVCPTELEDLANKYEEFKQLGVEVYSCSCDTHFVHKAWADASPA---IKK\n+VQYPMLADPSGALTRDLGILI---------------DDVHMAYRGSFVIN\n+PEGIIKIVELNDNSVGRDAEEILRKIKAAQYVAAHDGQVCPAKWREGQQT\n+LKPSIDLVGKI-----------\n+>431947.PGN_0660\n+---------------------------------------------M-T-P\n+ILNTVFPEFKLNAYHN---GE--FKVITNEDL---KGKWSLVVFYPGDFT\n+FVCPTELEDLANKYEEFKQLGVEVYSCSCDTHFVHKAWADASPA---IKK\n+VQYPMLADPSGALTRDLGILI---------------DDVHMAYRGSFVIN\n+PEGIIKIVELNDNSVGRDAEEILRKIKAAQYVAAHDGQVCPAKWREGQQT\n+LKPSIDLVGKI-----------\n+>879243.Poras_1036\n+---------------------------------------------M-Q-P\n+IINSSLPEFKVPAYTK---SKGF-HEVSNEDL---KGRWSVLFFYPGDFT\n+FVCPTELADLADNYAEFQQIGVDIYSVSTDSHFVHKAWQDASEA---VKK\n+VQYTMLADMRFELARAFGVMI---------------EEAGQAYRGTFLID\n+PDGKVRVAEIHDNGIGRDAQELLRKVRAAQFIYEHPGEVCPAKWRQGDAT\n+LKPSIDLVGKI-----------\n+>596327.PORUE0001_0881\n+-------------------------------------------MTM-Q-P\n+IINSNLPEFKVPAYTK---SKGF-HEVSNEDL---KGRWSVLFFYPGDFT\n+FVCPTELADLADNYAEFQQIGVDIYSVSTDSHFVHKAWQDASEA---VKK\n+VQYTMLADMRFELARAFGVMI---------------EEAGQAYRGTFLID\n+PDGKVRVAEIHDNGIGRDAQELLRKVRAAQFIYEHPGEVCPAKWRQGDAT\n+LKPSIDLVGKI-----------\n+>575590.HMPREF0156_01726\n+---------------------------------------------MAQ-T\n+IINSIMPNFKLQAYRK---GE-GFVTVSSDDL---KGKWAVLLFYPADFT\n+FVCPTELADMADHYEEFKKLGVEVYSVSTDTHFVHKAWADASEK---INN\n+IQYTMLADPTGNLCRAMGVMI---------------EEEGVAYRGTFLFN\n+PQGEVKVVEIHDNGIGRDASELLRKVKAAQFVAAHPDAACPAKWKEGDEV\n+LKPSIDLVGKI-----------\n+>203275.BFO_2700\n+---------------------------------------------M-E-P\n+IINSQIPEFKVQAFHN---GE-F-KTVSNKDI---EGKWAVFFFYPADFT\n+FVCPTELVDMAENYDQFKAMGVEIYSVSTDTHFVHKAWHDASES---IRQ\n+IKYPMLSDPTGLLSRAFGVMI---------------EESGMAYRGTFVVN\n+PEGKVKVAEIHDTGIGRNADELLRKVEAAQFVAENDGEVCPAKWKKGAST\n+LKPSIDLVGKI-----------\n+>226186.BT_2812\n+---------------------------------------------M-E-P\n+ILNSQLPEFSVQAFQN---GA-F-KTVTNNDL---KGKWAILFFYPADFT\n+FVCPTELVDMADKYAQFQEMGVEIYSVSTDSHFVHKAWHDASES---IRK\n+IKYPMLADPTGALSRALGVYI---------------EEEGMAYRGTFVVN\n+PEGKIKVVELNDNNIGRDASELLRKVEAAQFVATHDGEVCPAKWKKGEST\n+LKPSIDLVGKI-----------\n+>483215.BACFIN_04846\n+---------------------------------------------M-E-P\n+ILNSQLPEFSVQAFHN---GA-F-KTVTNNDL---KGKWAILFFYPADFT\n+FVCPTELVDMAEKYDQFKAMGVEIYSVSTDSHFVHKAWHDASES---IRK\n+IQYPMLADPTGALSRALGVYI---------------EEEGMAYRGTFVVN\n+PEGKIKVVELNDNNIGRDASELLRKVEAAQFVASHDGEVCPAKWKKGEST\n+LKPSIDLVGKI-----------\n+>709991.Odosp_2766\n+---------------------------------------------M-Q-T\n+IINSQLPEFSVQAFQN---GQ-F-KTVTDKDV---KGKWGIFFFYPADFT\n+FVCPTELVDMAEKYEQFQAMGVEIYSVSTDSHFVHKAWHDASES---IRK\n+IKYPMLADPTGALSRAFGVMI---------------EEEGMAYRGTFVVN\n+PEGQIKVVEIHDNNIGRDANELLRKVEAAQFVATHTGEVCPAKWKKGEAT\n+LKPSIDLVGKI-----------\n+>742767.HMPREF9456_00715\n+---------------------------------------------M-K-P\n+IINLQLPEFKVQAYHN---GA-F-KTVTHEDV---KGKWAIFFFYPADFT\n+FVCPTELVDVADKYDQLRAMGVEVYSVSTDSHFVHKAWHDASES---IRK\n+IKYPMLADTVGVLSRAFGVMI---------------EEEGMAYRGTFLLN\n+PEGQVKIAEIHDNGIGRNADELLRKVEAAQFVATHDGEVCPAKWKKGEET\n+LKPSIDLVGKI-----------\n+>547042.BACCOPRO_03297\n+---------------------------------------------M-T-S\n+IINSRIPEFKVQAFHN---GK-F-VTVSNEDL---KGKWAVFFFYPADFT\n+FVCPTELVDMAEKYEQFKAMGVEVYSVSTDSHFVHKAWHDASES---IRK\n+IQYPMLADPTGALSRAFGVMI---------------EEDGMAYRGTFVVN\n+PEGLIKLVEIQDNSIGRNADELLRKVEAAQFVAAHDGEVCPAKWKKGAET\n+LKPSIDLVGKI-----------\n+>435591.BDI_3396\n+---------------------------------------------M-E-P\n+IINSQLPEFKVQAFQN---GN-F-KTVTNEDV---LGKWAIFFFYPADFT\n+FVCPTELVDMAEKYEQFKSMGVEIYSVSTDSHFVHKAWHDASET---IRK\n+IQYPMLADPTGALSRAFGVMI---------------EEEGMAYRGTFLVN\n+PEGKIKVAEIHDNNIGRDASELLRKVEAAQFVASHDGEVCPAKWKKGEAT\n+LKPSIDLVGKI-----------\n+>411477.PARMER_03251\n+---------------------------------------------M-E-P\n+IINSQVPEFKVQAFQN---GS-F-KTVSSEDI---KGKWAIFFFYPADFT\n+FVCPTELVDMADKYGKFQEMGVEVYSVSTDSHFVHKAWHDASET---IRK\n+IKYPMLADPTGALSRAFGVMI---------------EEEGMAYRGTFLVN\n+PEGKIKIAEIHDNGIGRNADELLRKVEAAQFVASHPNEVCPAKWKKGEAT\n+LKPSIDLVGKI-----------\n+>435590.BVU_0847\n'..b'-FGEVCPVNWTQGQES\n+MQATREGVSSYLTKNMDNK---\n+>269798.CHU_2724\n+-----------------------------------------------M-S\n+LVGKKAPSFVAPAVLN---GYEV-VEAFSLDQY-LGKKYVVFYFYPKDFT\n+FVCPTEILAFQEKLAAFEAKDTVVVGCSTDTENSHFAWLSMPKNKGGIQG\n+VKYPLVADTAKTIATNYGVLGGNFD-IDDNGQM-IFVGAPIAYRGTFLID\n+KEGIVRHETVNDFPLGRNIDETLRMVEALQHVEK-FGEVCPANWGEGKEA\n+MKATVEGVSDYLAKN-------\n+>880070.Cycma_1830\n+-----------------------------------------------M-S\n+LVGKKAPLFSVPAVID---GEEI-VEDFSLEQF-IGKKDVIFFFYPKDFT\n+FVCPTEILAFQEKLEEFEKRGVAVIGASCDTEESHLAWLNTPKAEGGIQG\n+VTYPIIADPVKTVAHNFGVLAGDWN-YNEEGEL-TYQGLPVAYRATFLID\n+KEGTVRHETVNDLPLGRNIDEMLRLIDALRHVEK-YGEVCPANWEEGKEA\n+MSATREGVASYLSKN-------\n+>643867.Ftrac_1506\n+-----------------------------------------------M-S\n+LVGKKAPVFKTGAVIN---GEEI-VEEFSLEQY-IGKKDVIFFFYPKDFT\n+FVCPTEILAFQEKLAEFEKRGVAVVGASTDTEETHLAWLLTPQENGGIEG\n+VNYPLVADASKTIANNYGVLAGDWN-YNEEGEL-IFEGTPVAYRGTFFID\n+KEGIVRHETINDLPLGRNIDEMLRIVDAWQHVEK-YGEVCPANWEEGKEA\n+MEESRESVSSYLAKNKK-----\n+>388413.ALPR1_20723\n+-----------------------------------------------M-A\n+LVGKKAPAFSAGAVIN---GEEI-VENFNLDQY-LGKKNVVLFFYPKDFT\n+FVCPTELHAFQSKLAEFEKRDTVVIGCSTDTEETHLAWLMTPKAEGGIES\n+VTYPIIADASKTISLNYGVLAGEYS-YDPETNLWSFDGAPVAYRGTFLID\n+KEGVVRHESINDLPLGRNIDEYLRILDAQIHVEK-FGEVCPANWEEGKEA\n+MQATNEGVATYLSNN-------\n+>865938.Weevi_1165\n+-----------------------------------------------M-S\n+LVGKKAPNFVAPAVIN---GDEI-VENFSLP---IGEKNIVLFFYPKDFT\n+FVCPTELHAFQSKLAEFEKRDAVVIAASCDSEETHLAWLTTAKDNGGIEG\n+VTYPVVADLAKTIAMDYGVLAGDYV-YNEERDALEFEGLPVAFRGTFIID\n+KNGVVRHETINDLPLGRNIDEYVRLLDAILHVEK-YGEVCPANWEEGKEA\n+MNATKEGVATYLSKN-------\n+>926562.Oweho_1145\n+---------------------------------------------M-A-V\n+LVGKKAPQFTAAAVVN---GEEI-VDDFSLEQF-AGKKYVVLFFYPKDFT\n+FVCPTELHAFQSKLEEFRSLDVEVVAVSTDTEQSHWGWLQLTKDQGGIQG\n+VTYPLVADTNKTISANYDVLAGSYY-YDENDEL-KAEGEMIAYRGLFLID\n+KDQVVRHQLVNDLPLGRNVDEALRIVKALQFTEE-KGEVCPANWDEGKSG\n+MSATHDGVASYLSQN-------\n+>391603.FBALC1_09712\n+------------------------MLGVYVSLQPNFKFNIKKILKM-A-V\n+LVGKKAPQFNAQAVVN---GREF-VTDYSLDQF-IGKKHVVLFFYPKDFT\n+FVCPTELHAFQEKLEEFKSRNTEVVAVSTDTEQSHFGWLQMDKNQGGIKG\n+VTYPLVADTNKTISKNYDVLAGDYF-YDENDML-QAEGELIAYRGLFLID\n+KEGIVRHQIVNDLPLGRNVDEALRMVDALQFVEE-NGEVCPANWNKGKTG\n+MQATHEGVAEFLEKHVN-----\n+>694427.Palpr_1309\n+---------------------------------------------M-S-V\n+LVGKKAPVFNSKAVVN---GGEI-VENFSLEQF-VGEKYVVFFFYPADFT\n+FVCPTELIAFEDKAAEFAARNTVVIGASTDSEFSHWKWLQTPQNQGGIQG\n+VTYPLVVDQNLSISKNYDVLIGSEE-YDEEGNE-SFVGEPKAYRGLFLID\n+KQGVVRHQLVNDLPLGRNVDEVLRLIDALQFTEE-YGEVCPANWKKGEKA\n+LVATQEGIASYLSEKA------\n+>742766.HMPREF9455_02920\n+---------------------------------------------M-S-V\n+LVGKKAPVFKANAVVN---GNEI-VEGFSLEQF-KGKKYVVFFFYPADFT\n+FVCPTEIIAFQEKIAEFESRNVAVVGASTDSAFSHWKWLQTEQNDGGIKG\n+VKYPLVADQSLMISSAYDVLAGAFD-YNDEGED-VFNGAPQAYRGLFLID\n+KEGVVRHQVVNDMPLGRSVDEILRVIDALQFTEE-YGEVCPANWKKGDKA\n+LKATQEGISDYLSHKH------\n+>742767.HMPREF9456_01274\n+---------------------------------------------M-S-V\n+LVGKKAPVFNTSAVVN---GNEI-VEGFSLEQY-KGKKYVLFFFYPADFT\n+FVCPTEIIAFQEKIAEFESRNVAVVGASTDSAFSHWKWLQTEQNDGGIKG\n+VKYPLVSDQSLMISTAYDVLAGSFD-YNDEGED-VFNGAPQAYRGLFLID\n+KEGVVRHQVVNDMPLGRSVEEAIRVIDALQFTEE-YGEVCPANWKKGDKA\n+LKATQEGISDYLSHKH------\n+>435591.BDI_0094\n+---------------------------------------------M-K-A\n+LIGKKAPEFHAPAVVN---GNEI-IEDFSLEQY-VGKKYVVMFFYPMDFT\n+FVCPTELHAFQQKLQEFERRNVAVVGCSVDSQFSHFAWLNQDKNKGGIHG\n+VTYPLVSDFSKTISENFGVLAADYI-TNESGEL-ISRGNPVAYRGLFLID\n+KEGLIRHYVINDLPLGRNVDEALRMVDALQHFEE-YGEVCPANWSKGKDA\n+MKATNAGVSNYLSH-H------\n+>679937.Bcop_1401\n+---------------------------------------------M-R-S\n+LIGRKAPKFSAAAVIN---GGEI-VQDFSLEQY-IGKKYVVFFFYPMDFT\n+FVCPTELHAFQEKIDEFEKRGVAVVGCSVDSEQSHWAWLNTPKNEGGIQG\n+VKYPIVADFSKEISEKFGVLAGRYA-PDENGDW-VIDGAPVAYRGLFLID\n+KEGTVRHCVINDLPLGRSVDEAIRVVDALQHFEE-YGEVCPANWSKGKEA\n+LKDTHEGVADYLSE-H------\n+>272559.BF2360\n+---------------------------------------------M-R-S\n+LIGKQAPKFDATAVIN---GHEI-VQNFSLDQY-KGKKYVVFFFYPMDFT\n+FVCPTELHAFQEKLEEFEKRDVAVVGCSVDSEYSHFSWLQMPKNEGGIQG\n+VKYPIVSDFSKSISESYGVLAGSYA-PDENGNW-VCEGTPVAFRGLFLID\n+KEGVVRHCVINDLPLGRNVDEVLRMVDALQHFEE-YGEVCPANWSKGKDA\n+MKATEDGVANYLSK-H------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1694 @@\n+>50743.SCB49_11674\n+-----------------MPIP----K-INPTTTNAWQKLEAHFEAIYDVH\n+IQ---ELFASEKGRRKSMSFVWEDVSLDYSKNRISAETFQLLLQLAEECK\n+LKEAIDAQYNGETINETEGRAVLHTALR---------DFKNLKPEVEAAL\n+EKMRDFSEKIISGDWKGHTGKAITDIVNIGVGGSSLGPAMTTEALS-FY-\n+K----------N-HLNIHYVSNVDGDHVMETLKKLDPETTLFIVVSKSFT\n+TQETLTNANTIRKWFVKN---ISE--TAIANHFVAVSANNTEAQKFGISE\n+D--NIFPMWDWVGGRFSLWSAVGLSTCCSVGYEHFEALLKGAHAMDEHF-\n+KDTSFDKNMPVIMAMLSVWYNNFFQTETEMVLPYSQYLSKLVNHLQQAVM\n+ESNGKSIDRNGAPVEYQTGTVIWGSTGVNAQHAFMQLLHQGTKLIPTDFI\n+C----FETSLYEVEEHQEKLLANCYAQADALAKGTFGKQVENN------F\n+----------KRFEGNSPSNMLKIEKLTPNSLGKLIALYEHKLFVQGVIW\n+NIYSYDQWGVELGKKMANDILSK--------------------SRI----\n+---\n+>156586.BBFL7_01801\n+-------------------MK----N-INPTETNAWLQLEKHFEGFDDFS\n+LR---EEFKKDASRAQKLTIIDKDFYVDFSKNLITESTRTHLTALATECG\n+LKEAINSYFTGAVINATEKRSVLHTALRTPQAHADKSLESNVSDAIAS-K\n+QKMFDYVDGILNGDTLSANGKKFDTIVNIGIGGSDLGPVMIYEALQ-AY-\n+K----------N-NMTLHFVSNVEGDHVEEVLKKINPDTTLFVIVSKSFG\n+TQETLTNATTIRNWFTE---KLEA--SAVSKHFIAVSSNVDKAVNFGIDH\n+K--NIFPMFDWVGGRFSLWSTVGMSVALGIGTDNFQALLDGAHEMDNHF-\n+RNTDFEKNIPVQLALMTIWYNNFYRAQSEVIIPYTQYLHRLPAYLQQAIM\n+ESNGKCVDRDGNSVTYDTGNIVWGEPGTNSQHAFFQLIHQGTKLIPAHFI\n+A----FAKAKYNQPDHHNKLMANFIAQTEALMNGKTRSEAKKDLERSGKS\n+KDEIDMLLPFKVFEGDQPTTTILIDELTPQSIGKLIAMYEHKIFTEGIIW\n+NIYSYDQWGVELGKVLADTILDNIENKEY-ADHD--SSTSAILKRFGNLN\n+S--\n+>313595.P700755_17689\n+-----------------MPLH----T-KSPLDSKHWKALET--LSKKDYD\n+LK---PLFASNSNRFKDFSIHSDDFLVDYSKNLLDKEVLDHLIHLAKEAG\n+LDEAINSYFEGDLINQTEGRAVLHTALRASKNNSAKVEGKDVYGDVQEVL\n+SKIKDFADQVNSGERVSFSGDKFTDVVNIGIGGSDLGPQMIVDALA-YY-\n+Q----------K-DIKPHFVSNVDGDHVMETIKGLNPKTTLFLIVSKSFT\n+TQETLTNANTLRDWFLK---SASL--QDVKHNFVAVSTNIKAVENFGIDK\n+D--NIFPMYDWVGGRFSLWSAAGLSIAVSLGSKHFQELLEGAEEMDHHF-\n+KTTDFKTNIPVILALLGIWYNNFLKAESEAVIPYTQYLQKLASYLQQASM\n+ESNGKSVDRTGQKTTYQTGTLVWGEPGTNSQHAFFQLIHQGTKLIPSDFI\n+G----YKIPLHGNKEHHDILMANYFAQTEALMIGKSKEEVTKELQDLGMK\n+EKDIQKLLPFKVFEGNKPTTSILMDKLTPKSLGKLVAMYEHKIFVQGVIW\n+NIFSYDQWGVELGKQLAKNTLKDIQSSTIEGSHD--ASTNALLKHFKA--\n+---\n+>487796.Flav2ADRAFT_0649\n+---------------MQKILP----N-TNPTELNAWESLKKHFQNTKQTT\n+LK---EYFENEPNRLDYSILKWRDFYVDFSKNRLDKKGFDLLLQLAEESG\n+LKKAIDAQFSGSKINVTEDRAVLHTALRSITKDPVLFEGENVLPSLANTQ\n+KKMYAFCDKVISGAWKGYTGKEITHIVNIGIGGSDLGPAMVVEALE-YY-\n+K----------N-QLDVRFVSNVEGDHHQEIIKDLNPETTLFVIVSKTFT\n+TQETLSNANSIRTWFLN---QAPK--DAIAKHFVAVSTNTEKTAAFGISS\n+E--NTFPMSDWVGGRFSLWSTVGLSICLAVGPKNFTKLLEGAGQMDYHF-\n+QNTPFDKNIPVVLALISIWYNNFWTAESEAIIPYTQYLRNLPAYLQQGIM\n+ESNGKSVGRDGKKVNYQTGTLIWGASGTNAQHAFFQLIHQGTKLIPADFI\n+G----FKKALHGNKDHQEKLLANFIAQTEALMNGKTLDQVKIELSASGLS\n+TEEQNKIAPFKVFEGNKPTNTLLIDSLTPASLGSLIALYEHKIYVQGILW\n+NIYSYDQWGVELGKQLANVVLEDIKDNAQ-HPHD--ESTKALLKHIAN--\n+---\n+>313598.MED152_09385\n+-----------------MALP----N-NNPTKTNAWQQLTNHFNEIKDIK\n+IQ---DLYK-DENRKEDFTLALKDLTVDFSKNRITSETIKLLVDLAEEVG\n+LKQAIESQFNGEVINVTEGRAVLHTALRSNSEDAVLVDGKNIKPQIQTAL\n+RKIRSFSNKVISGKWKGYTGKSITDIVNIGIGGSDLGPDMIVESLQ-YY-\n+K----------N-HLNTHFVSNVDGDHVSEIIKRLNPETTLFVIVSKTFT\n+TQETITNAETIKNWFLK---SATI--FDIPKHFVAVSTNLEAVDNFGIDK\n+K--NVFPMWNWVGGRFSLWSAVGLSISLSVGFDNYRALLDGAEEMDIHF-\n+RNQDFESNIPVVLALLSIWYNNFYMAETEAVLPYSQYLKKLPDYLQQAIM\n+ESNGKGVDRNGEKIDYQTGTIVWGSTGTNMQHAFMQLVHQGTKLIPADFI\n+G----YKESLYGLTDHHKKLMANYYGQMDALAFGKTKEEVHLELQFSGN-\n+TEQINTLLPFKVFEGNRPSNSILFDKLTPKSLGKLVALYEHKIFTQGILW\n+NIYSYDQFGVELGKELAKKLLDKQ--------------------------\n+---\n+>313594.PI23P_04837\n+M-----------LKNNSMALK----N-INPTKTSAWGKLTAHFGENKNKT\n+IK---DLCK-DPMRKEDFSVVLGDLSVDFSKNRIDKETISLLVALAEEVG\n+LRDAIEKQFNGEIINVTEGREVLHTALRSTSEDPVYVAGKNIKPQIQTAL\n+RKIKSFSNKVVSGKWKGYTGKSITDIVNIGIGGSDLGPDMVVESLQ-YY-\n+K----------N-QLTTHFVSNIDGDHVSEVMKKLNPETTLFVIVSKTFT\n+TQETITNAETLKNWFLK---SATI--FDIPKHFVAVSTNLEAVDNFGIDK\n+S--NVFTMWNWVGGRFSLWSGVGLSISLSIGYDNYRALLDGAEEMDLHY-\n+RNTPFEKNIPVILALLSIWYNNFYGAETEAVLPYSQYLKKLPDYLQQAIM\n+ESNGKGVDRNGDVVDYQTGTIVWGSTGTNMQHAFMQLVHQGTKLIPADFI\n+G----YKESLYGLTEHHKSLMANYYGQIEALAYGKTKEAVHLELKFSGD-\n+QEKIEKLLPFKVFEGNRPSNAIVFDKLTPHSLGKLVAMYEHKIFTQGILW\n+NIYSYDQFGVELGKELAKKFLTAQ--------------------------\n+---\n+>1041826.FCOL_09980\n+-----------------MTFP----S-VNPTKTNAWNKLKEHFIDVKGIS\n'..b'GTQLAH--VDGGVPNMRIVLPELSEYNIGGLLYFFEKACGISGYLL\n+GVNPFNQPGVEAYKKNMFALLNK-------PGYEEE--SKAIQAKL----\n+---\n+>483215.BACFIN_06411\n+-----------------M---------INLNIEKTFGFISKEKVSAYEAE\n+VKAAQEMLEKGTGKGNDF-LGWLHLPSSITKEHL-ADLNATAKVLRDNCE\n+V-------------------------------------------------\n+-------------------------VIVAGIGGSYLGARAVIEALSNSFT\n+W-LQN-K-K-AD-PIMIYAGHNISEDYLYELTEYLKDKKFGVINISKSGT\n+TTETALAFRLLKKQCEDQ---RG--KETAKKVIVAVTDAKKGAARVTADK\n+EGYKTFIIPDNVGGRFSVLTPVGLLPIAVAGFD-IEKLVAGAADMEKACG\n+SDVAFAENPAAIYAATRNELYRN-GKKIEILVNFCPKLHYVSEWWKQLYG\n+ESEGKD----------NKGIFPASVDFSTDLHSMGQWIQEGERSIFETVI\n+SVEK-VNHKLEVPSDEANLDGLNFLA-------GKRVDEVNKM-------\n+-AELGTQLAH--VDGGVPNMRIVLPELTEYNIGGLLYFFEKACGISGYLL\n+GVNPFNQPGVEAYKKNMFALLNK-------PGYEEE--SKAIQARL----\n+---\n+>411476.BACOVA_03233\n+-----------------M---------ISLNIEKTFGFISKEKVFAYEAE\n+VKAAQEMLEKGTGKGNDF-LGWLHLPSSITKEHL-ADLNATAKVLRDNCE\n+V-------------------------------------------------\n+-------------------------VIVAGIGGSYLGARAVIEALSNSFT\n+W-LQE-K-K-TA-PVMIYAGHNISEDYLYELTEYLKDKKFGVINISKSGT\n+TTETALAFRLLKKQCEDQ---RG--KETAKKVIVAVTDAKKGAARVTADK\n+EGYKTFIIPDNVGGRFSVLTPVGLLPIAVAGFD-IDKLVAGAADMEKVCG\n+SDVAFAENPAAIYAATRNELYRN-GKKIEILVNFCPKLHYVSEWWKQLYG\n+ESEGKD----------NKGIFPASVDFSTDLHSMGQWIQEGERSIFETVI\n+SVEK-VNHKLEVPSDEANLDGLNFLA-------GKRVDEVNKM-------\n+-AELGTQLAH--VDGGVPNMRIVLPELSEYNIGGLLYFFEKACGISGYLL\n+GVNPFNQPGVEAYKKNMFALLDK-------PGYEEE--SKAIRAKL----\n+---\n+>657309.BXY_11650\n+-----------------M---------ISLNIEKTFGFISKEKVFAYEAE\n+VKAAQEMLEKGTGKGNDF-LGWLHLPSSITKEHL-ADLNATAKVLRDNCE\n+V-------------------------------------------------\n+-------------------------VIVAGIGGSYLGARAVIEALSNSFT\n+W-LQE-K-K-TA-PVMIYAGHNISEDYLYELTEYLKDKKFGVINISKSGT\n+TTETALAFRLLKKQCEDQ---RG--KETAKKVIVAVTDAKKGAARVTADK\n+EGYKTFIIPDNVGGRFSVLTPVGLLPIAVAGFD-IDKLVAGAADMEKVCG\n+SDVAFTENPAAIYAATRNELYRN-GKKIEILVNFCPKLHYVSEWWKQLYG\n+ESEGKD----------NKGIFPASVDFSTDLHSMGQWIQEGERSIFETVI\n+SVEK-VNHKLEVPSDEANLDGLNFLA-------GKRVDEVNKM-------\n+-AELGTQLAH--VDGGVPNMRIVLPELSEYNIGGLLYFFEKACGISGYLL\n+GVNPFNQPGVEAYKKNMFALLDK-------PGYEEE--SKAIRAKL----\n+---\n+>203275.BFO_3358\n+-----------------M------K-TITLDIDKVLGAVTRKQIDALAPK\n+VTQSMEMLHKGTGPGNDF-LGWLNLPSSITDEEL-KDIEKTASQLR-KCK\n+A-------------------------------------------------\n+-------------------------VVVIGIGGSYLGTRAVVEALNNSFD\n+G-LQTSK-R-K-NPVLLYAGNNIGEDYLFELCATLDGKKFGIINISKSGT\n+TTEPAIAFRILKKQLETN---IG--VEEARKYIVAVTDRSRGALRTLADK\n+EGYKTFVIPDDVGGRYSVLTPVGLLPIAVAGID-IRTLVQGAVDMEKATD\n+VKKLFDQNIAAIYAVTRNALYDK-GKKIEILANFHPKLHYIGEWWKQLYG\n+ESEGKD----------HKGIFPASVDLTTDLHSMGQWIQEGERTIFETVI\n+SIAK-PDHKMTIPSDKADLDGLNYLA-------GKRIDEVNKM-------\n+-AELGTQLAH--VDGGVPNIKITLPELNAYYIGQLFYFFEKACGISGYLL\n+GVNPFDQPGVEAYKKNMFALLDK-------PGYEKE--SKAIRKKLK---\n+---\n+>435591.BDI_0148\n+-----------------M------K-NISLNIDKALGTVSKEQVYAQEAK\n+AMECIATLHNGNGAGNDF-LGWLHLPSSITDAEL-ADIENTANVLRSKCE\n+V-------------------------------------------------\n+-------------------------VVAIGIGGSYLGTKAVVEALNNSFD\n+W-LQN-D-R-K-NPVMLYAGHNIGEDYLYELSEVLKGKQFGIINISKSGT\n+TTEPALAFRILKKQLEDA---VG--KEEAKHRIVAITDAKRGALRTLADQ\n+EGYKTFIIPDNVGGRFSVLTPVGLLPIAVAGIS-IRDLVAGAVSMEKATD\n+ASVPFADNMAAIYAATRNELYKN-GKKIEILANFHPKLHYIAEWWKQLYG\n+ESEGKD----------GKGIFPASVDLTTDLHSMGQWIQDGERTIFETVI\n+SVEA-TDHSVLVPTDEADLDGLNFLA-------GKHVDEVNKM-------\n+-AELGTQLAH--VDGGVPNIKVNMPEVSAFYIGQLFYFFEKACGISGYML\n+GVNPFNQPGVEAYKKNMFALLNK-------PGYEKE--SEAIKARL----\n+---\n+>411477.PARMER_02970\n+-----------------M------K-NISLNIDKALGTVTKEQVYAQAAK\n+AHECNATLQNGNGAGNDF-LGWLHLPSSITDAEL-TDIENTANVLRSKCE\n+V-------------------------------------------------\n+-------------------------IVAIGIGGSYLGTKAVVEALNNSFD\n+W-LHT-N-R-K-NPVLVYAGHNIGEDYLYELCEILKGKQFGLINISKSGT\n+TTEPALAFRMLKKQLEDA---VG--KEEAKHRIVAITDAKRGALRTLADQ\n+EGYKTFIIPDNVGGRFSVLTPVGLLPIAVAGIS-IRDLVAGAISMEKATD\n+VSVPFAENMAEIYAATRNELYKS-GKKVEILANFHPKLHYIAEWWKQLYG\n+ESEGKD----------GKGIFPASVDLTTDLHSMGQWIQDGERTIFETVI\n+SVEE-PNHKVVVPTDEANLDGLNFLA-------GKRVDEVNKM-------\n+-AELGTQLAH--VDGGVPNLKITMPEVSPYYIGQLFYFFERACGISGYML\n+GVNPFDQPGVEAYKKNMFALLNK-------PGYEKE--SEAIRARL----\n+---\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,492 @@\n+>518766.Rmar_0742\n+------------------MKDIIRGLAYV----VGDSIDTDQIIPAQHLV\n+YSLTRPEERRL--YGRYALSGVPAEG-QGLPFGNIPFTEPDAYKSRFKIV\n+VAGKNFGCGSSREHAPFALQEAGCEAVVAESYARIFYRNAIDGGFVVPFE\n+TPVRLIDKI------RTGDELEIDTRLAKLT--NLTT----GEE----FL\n+LHP---------L-GEVAEIL-RAGNLFEYA-R-KAGLIPTNA----\n+>309807.SRU_2152\n+MPTA--------------TDNTVTTVTGPAVSVRGNDIDTDQIVPARFLK\n+-----EVTFDN--MGEYAFYDVRRDD-DGSLN-DHPFN---RYPNA-TIL\n+VVNENFGCGSSREHAPQALMRWGIDGLIGESFAEIFAGNCQALGL-PTAT\n+ADHETVEWIMAQVTADPALELTIDVEAETVT--VSD------EP--VDVT\n+ISDAQREALLQGVWDTTALMKSYMDEVEQTA-D-RLPYLNEFADC--\n+>595499.SMDSEM_045\n+-------------------MEKFITLISRAVPIYLENIDTDQIIPARFLK\n+LTKK-----IN--FGKNLFKDWRFDQ-KGNLIKNFILNHEK-FY-GE-IL\n+ITGKNFGCGSSREHAAWAIRDYGFKVVISNYFADIFKQNALNNGL-LIIE\n+LKNTFLKFILKKILLNPNLFIEINLEHQYVK--IEK------KK--EFFK\n+IDDFIKKCFINGY-DEIEYILNLKKKFKNFE--KKIYYY--------\n+>641892.DMIN_00390\n+-------------------MEKFITLFSTAVPLFIDNIDTDQIIPARFLK\n+LTTK-----SD--FGKNLFRDWRYDS-NGKIKKNFILNKKK-YS-GN-IL\n+ITGKNFGCGSSREHAAWAIRDYGFKVVISNIFADIFKQNALNNGL-LTIE\n+LKKDFINLIYKKIFLNPNILFEINLEQQYVK--FEN------NK--ELFK\n+IDDFKKKCFINGY-DDIELLFSIKKKIEIFE--KKNIYN--------\n+>706194.SMCARI_049\n+-------------------MEKFITLFSTAVPLDIENIDTDQIIPARFLK\n+LTTK-----SD--FGKNLFRDWRYNS-NGKINKNFILNNKN-YS-GK-IL\n+ITGKNFGCGSSREHAAWAIKDYGFKVVISNFFADIFKQNALNNGL-LTIE\n+LKKTFLNLILKKLYLNNNLIFSINIENQYVK--IEN------NK--EYFQ\n+IDDYKKKCFINGY-DDIEFLLSLKKKIKDFE--KKNLYN--------\n+>331104.BLBBGE_069\n+-------------------M-----LISQAIPLPIEDIDTDQIIPARFLK\n+EIKR-----EE--CGKNLFIDWRYKK-DGSLNKDFVFNNSN-FF-GK-IL\n+LSGRNFGCGSSREHAAWSLYDYGFRVIISSFFADIFRENALNNGL-LTVE\n+VSKCFLNKLFDIINKNPRTQIKVDLINQKVT--IMET----GEF--YQFY\n+IHPYKKNCFLNGY-DDIDFLVSIKKDVEYFE--KNRKSVPF------\n+>600809.BPLAN_565\n+-------------------MKKFTVITSKAVPLPVEDIDTDQIIPARFLK\n+EAKR-----EE--YGKNLFRDWRYSN-DGSLKKDFILNNPL-FS-GK-IL\n+LSGRNFGCGSSREHAAWALFDYGFQVVISSFFADIFKENALNNGL-LTVE\n+ISEKFLKNLFDLVNKKPDTNIKVDLIEQLIT--IMET----GIS--EKFY\n+IHPYKKNCFINGY-DDIDFLVSIKKDIENFE--KKTNSFKI------\n+>643867.Ftrac_1643\n+-M------------------EKFNTLNSQAVLLPFEDVDTDQIIPARFLK\n+SVSR-----EG--FGENLFRDWRYLE-DGSPNPEFVLNQEG-NK-GD-VL\n+VAGRNFGCGSSREHAAWALVDYGFKAVVSSFFADIFKNNALNNGL-LPVQ\n+VTDDFLAQVFQILKNRPEAKLQIDLNEQEIS--LVGS----ALT--ESFE\n+INSYKKYCLQNGF-DDIDFLLNKRAEIEAYE-Q-SLA----------\n+>525257.HMPREF0204_13895\n+-M------------------QKLIIIKSTAVPLPAENIDTDQIIPARFLK\n+SIDR-----KG--FGENLFRDWRFNIHTGEPNPDFVLNNPK-FS-GE-IL\n+VAGNNFGCGSSREHAAWALTDYGFKVIISSYFADIFKGNALNNGL-LPVK\n+VSEGFLKEILEGINENPDQEIAIDVELQSVS--FKD------VT--ETFE\n+LDSYKKICLLNGY-DDIDFLISRKKAITEFELK-TQKTNERQLF---\n+>391587.KAOT1_15177\n+-M------------------STFNTFTSTAFPLAVENIDTDQIIPARFLK\n+ATSR-----DG--FGENLFRDWRYHK-DGSLNADFVLNQQQ-YS-GS-IL\n+VAGHNFGCGSSREHAAWALKDFGFNVIISSFFADIFKGNALNNHV-LPIQ\n+VTPAFLAKLLVAIQENPNTEIEVNLEAQTVA--FG-------KE-KASFD\n+INPYKKMCLQKGY-DDIDFLVSNLSKIKAFE-Q-QHIY---------\n+>313606.M23134_05908\n+-MLLEANCLLLFLNQKIMKDSSFGLLQTTGVPVKVENVDTDQIIPARFLK\n+AISR-----EG--FGENLFYDWRYDN-EGNPKPDFILNQPG-ND-GQ-VL\n+VGGKNFGCGSSREHAAWAIKDYGFKAVISSFFADIFKGNALNNGV-LPVQ\n+VSDAFLARLFDLMEQDATTPIAIDLEAQTVAVTNKQT----GETMTEIFE\n+INEYKKMCLQKGY-DDIDYLLSLQTQVETYE-K-NKAVY--------\n+>908612.HMPREF9720_0162\n+-M----------------SIPKFETFTSGAVPVRTENIDTDQIIPARFLK\n+ATER-----KG--FGDNLFRDWRYDA-EGRKVASFPLNDSR-YE-GR-IL\n+VAGRNFGCGSSREHAAWAIADYGFRVVVSSFFADIFRNNALNNGL-LPIT\n+VSDNFLAAIFAAIADDPAARFTVDLEGQTLT--AEAT----GRS--ERFE\n+IDAYKKRCLQNGY-DDVDYLCSISDQIRRFE-A-ARK----------\n+>717959.AL1_28200\n+-M----------------SIPKFVTFTSGAVPVEVENIDTDQIIPARFLK\n+ATER-----KG--FGDNLFRDWRYDA-AGQRIASFPLNDPR-YE-GR-IL\n+VAGRNFGCGSSREHAAWAIADYGFRVVVSSFFADIFRNNALNNGL-LPIR\n+VSEEFLKAVFGEIRRDPKAQFTVDLGNQTLT--IVSD----GRS--EGFE\n+IDAYKKRCLENGY-DDVDYLRSIADRIEAFE-A-ARK----------\n+>709991.Odosp_2902\n+-M-----------------INQFTTLTSTAIPLKIENVDTDQIIPARFLK\n+ATTR-----EG--FGKQLFFDWRYDA-QGNPKTDFVLNSPD-YT-GE-IL\n+IAGKNFGCGSSREHAAWAIYGAGFKVVISSFFADIFRNNALNNGL-LPVQ\n+VSESFLAKLFQVVRSAPSTTVSIDLERQTVT--LTAT----GEQ--ELFE\n+ISPYKKECLLKGY-DDVDYLMSIHHKIEAFE-K-TR-----------\n+>760192.Halhy_2014\n+-M----------------AREKFHLVHSSAVPVHIENVDTDQIIPARFLK\n+ATTR-----DG--FGENLFRD'..b'\n+TSEGCLSELFASIHNNPKATVTVNLEEQTIR--NNET----GTS--ESFE\n+INSYKKECLLKGL-DDIDFLLSNQSLTEAWE-SRANRF---------\n+>694427.Palpr_0055\n+-------------------MEKFITLTSSVVPLPIENVDTDQIIPARFLK\n+ATNK-----DG--FGDNLFADWRYNK-DGSPKADFVLNNST-YS-G-SIL\n+VAGKNFGSGSSREHAAWAIDGYGFKVVVSSFFADIFRGNALNNGV-LPVV\n+VTPEFLAEVFSCVNADPKTTLTIDLKNQTVS--NNAT----GKS--ETFE\n+INAYKKECLLNGL-DDIDYLLSKKEQIEQFE-K-ARV----------\n+>742766.HMPREF9455_00151\n+-------------------MEKFQTLTSTYVPLPIENVDTDQIIPARFLK\n+ATDK-----EG--FGNNLFADWRYNK-DGSPKADFVLNNPT-YS-G-QIL\n+VAGKNFGSGSSREHAAWAVAGYGFRAVVSSFFADIFRNNSLNNGV-LPVV\n+VTPEFLAEIFASVNADPKATLTIDLENQTIT--NNAT----GKL--ESFE\n+INPYKKECLLKGL-DDIDYLLSKKEMTEEYE-K-EHTL---------\n+>742767.HMPREF9456_01623\n+-------------------MEKFQTLTSTYVPLPIENVDTDQIIPARFLK\n+ATDK-----EG--FGDNLFADWRYNK-DGSPKADFVLNDST-YS-G-QIL\n+VAGKNFGSGSSREHAAWAVAGYGFKAVVSSFFADIFRNNSLNNGV-LPVV\n+VTPEFLSEIFACVNADPKATLTINLEKQTIT--NNVT----GKT--ESFE\n+INPYKKECLLKGL-DDIDYLLSKKELTEKYE-T-ERPL---------\n+>411154.GFO_2097\n+-M------------------EKFITLKDTVVPLDAENVDTDQIIPARFLK\n+ATDK-----EG--FGENLFRDWRFDK-NGDPIEDFVLNQDK-YS-GS-IL\n+LAGNNFGCGSSREHAAWAIKAYGFKAVVSSYFADIFKGNALNNGL-LPVQ\n+VCPEFLTKLFVAIEKDQNEKISIDLEAQKIK--IESS----GES--ESFD\n+IDSYKKTCLINGY-DDIDFLTSKLEAIKKFE-QKRRGKENVPQ-ETI\n+>655815.ZPR_1692\n+-M------------------EKFTTLQDTAVPLEVENIDTDQIIPARFLK\n+ATDK-----AG--FGENLFKDWRFDK-DGKPVEDFSLNQDQ-YS-GQ-IL\n+IAGNNFGCGSSREHAAWALKAYGFKVVVSSYFADIFKGNALNNGL-LPVQ\n+VSPEFLDELFLAIKKDNKESFKVDLENQKIQ--IISS----GKS--ENFA\n+IDAYKKTCLINGF-DDIDFLVSKLDAIKKFE-E-KQTQMREAAIQ-E\n+>50743.SCB49_05305\n+-M------------------EKFTKITSTAVPLDIENIDTDQIIPARFLK\n+ATDK-----QG--FGNNVFRDWRYDN-LGNVNPEFIFNNPS-YK-GK-IL\n+VAGNNFGCGSSREHAAWALVDYGFKVIVSSYFADIFKGNSLNNGL-LPIQ\n+VSETFLKKLMEILIAEPTVQLEVDLEKQHIS--VIEK----NIS--EFFE\n+IDTFKKNCLINGY-DDIDFLLSKREAIKEFE-L-SRN----------\n+>398720.MED217_10954\n+-M------------------EKFTKLTDTAVPLPIENIDTDQIIPARFLK\n+STDK-----KG--FGDNVFRDWRFDQ-KGEKNEDFVLNDPT-YS-GP-IL\n+VAGDNFGCGSSREHAAWAIAGYGFKVVISSFFADIFKGNALNNGI-LPIQ\n+VTPEYLKELLALVTEKPDTKLTIDLENQLLS--TPA--G---KL---EFE\n+IDPYKKVCMINGY-DDIDFLISKKEKIEAFE-Q-ERSF---------\n+>313590.MED134_11966\n+-M------------------EKFTKLVSTAVPLPIENIDTDQIIPARFLK\n+ATDK-----KG--FGDNVFRDWRFKK-DGTLDAEFPINKPQ-YA-GAKIL\n+VAGDNFGCGSSREHAAWAIVGYGFKVVISSFFADIFKGNALNNGL-LPIQ\n+VTPEYLKELLAGIEANPELPITIDLENQVVE--MAEVYAEQGRSTKAEFE\n+IDPYKKVCMINGY-DDIDFLLSKKAEIEAFE-K-ERMVF--------\n+>983548.Krodi_2179\n+-M------------------EKFTKLISTAVPLAIENIDTDQIIPARFLK\n+ATDK-----KG--FGDNVFRDWRFKK-DGTLDAEFPINKPQ-YA-GAKIL\n+VAGDNFGCGSSREHAAWAIVGYGFKVVISSFFADIFKGNALNNGL-LPIQ\n+VTPEYLKELLANIEANPKLPITIDLENQVVE--MAVVYAEQGRSKKAKFD\n+IDPYKKVCMINGY-DDIDFLLSKKAEIEAFE-K-ERMVF--------\n+>1034807.FBFL15_2593\n+-M------------------EKFIKLKSKAVPLPIENIDTDQIIPARFLK\n+VTDK-----VG--FGNHLFKDWRFDD-HNLPITSFVLNNND-YS-GA-IL\n+VAGDNFGCGSSREHAAWALADYGFKVVVSSYFADIFKGNALNNGI-LPIL\n+VSPDFLKQIFDHIQADSQTNLIVDLENQEIA--IENT----PLK--EPFE\n+IDPYKKICMINGF-DDIDFLISKKAEIEAFE-K-NR-----------\n+>926562.Oweho_2471\n+-M------------------EKFVKLHSTAVPLPIENIDTDQIIPARFLK\n+ATNK-----VG--FGANLFRDWRYDG-EGKPLTNFVLNDLT-YG-GH-IL\n+LAGDNFGCGSSREHAAWALADYGFKVVVSSYFADIFKGNALNNGI-LPIQ\n+VSPEFLAEALDRVRRNPCLKIVVDLENQTIS--VEE------LN--EHFE\n+IDSYKKLCLMNGY-DDIDFLISRKTKIEAFE-A-SKSLSYGV-----\n+>313595.P700755_00452\n+-M------------------EKFTTLNSRAIPLDIENVDTDQIIPARFLK\n+TTSR-----EG--FGENLFRDWRYDK-KGSERSDFILNDKL-YS-GS-VL\n+IAGDNFGCGSSREHAAWALSDYGFKAIVSSFFADIFKGNALNNGL-LPIQ\n+VSPDFLKKIMKLISEKPETLVRVDLESQTIS--IENS----KLK--ESFK\n+IDTYKKTCMINGY-DDIDFLLSKKNKIEHFE-N-QRKLLNVYD----\n+>391603.FBALC1_02737\n+-M------------------EKFTTLKSTAIPLNIENVDTDQIIPARFLK\n+ATDK-----KG--FGDNVFRDWRYNK-DGSENSEFILNDSK-YS-GS-IL\n+VAGDNFGCGSSREHAAWAIVGYGFKVVVSSFFADIFKGNALNNGL-LPVQ\n+VSETFLSDLLSKIVSNPETEIDVNLEKQTIS--IVGS----DTS--EDFE\n+IDAYKKTCMINGY-DDIDYLINNKEQIEAFE-A-HKIY---------\n+>983544.Lacal_0597\n+-M------------------EKFTTLHSKAIPLQIENVDTDQIIPARFLK\n+ATDK-----QG--FGDNVFRDWRYNK-DNTLNIDFALNNPN-HS-GS-IL\n+VAGDNFGCGSSREHAAWALTGYGFKVVVSSFFADIFKGNALNNGL-LPVQ\n+VSKAFLNTLFKSIKKDSNINIIVNLEAQTIA--IENT----EHV--AHFE\n+INSYKKTCLINGY-DDIDFLLSKKAKIEAFE-I-SLN----------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,480 @@\n+>992406.RIA_1301\n+--------------MKRKSWLIVGILGVVIFGLGMLANSIMQRKAES-MH\n+LSKANNNIKD-FESRNEIWGDSYPREYESWAKTADTTFRSKHMSSNADDL\n+LEERPEMVILWAGYAFAKDYKAPRGHFYSVKDVVGTLRTGAPDA-NHPDV\n+QPGTCWTCKSPDVPRMMNQMGVENFYKAKWSQLGSDVVNPIGCADCHDPK\n+TMNLTITRPALVEAYQRMGKDIKKATHQEMRSLVCAQCHVEYYFKG-D--\n+---NKYLTFPWDKGMSLENMEEYYDNAKHVDFVHKLSKAPILKAQHPDFE\n+VYNLGIHAQRGVSCADCHMPYKSEGGVKYTDHHISSPLANINNTCQVCHR\n+ESETTLAQNVYERQDMVFQLRNRLEKQLAKVHLMAKFLWDNNATEQEMKP\n+VLDLIRKSQWRWDFITASHGAAFHAPLESQRILGDGLYLAVQAEAKMNDI\n+SNKKNISGKFVMPDVSTKAKAQKFIGLDIPKESAAKAQFMKTVVPEWLKK\n+AKAKGVLVKDK-------\n+>860228.Ccan_18600\n+--------------MKKKNWLIVGILAVVTFLLGMLANSIMGRKAEA-QI\n+ISRANTDIKD-FEARNEIWGEYYQREYQSWLQTADTTFRAKYMSSDNDDL\n+LAERPEMVILWAGYAFSKDYTAPRGHMHAVADVTHTLRTGSPTD-STHSP\n+QPSTCWTCKSPDVPRMMNKIGIENYYKGHWDDLGSEIVNPIGCANCHDPK\n+TMNLTITQPALVEAFNRQGKDITKATHQEMRSLVCAQCHVEYYFKK-E--\n+---SNYLTFPWDHGKKVEDIEKFYDNVAWTDFVHKVSRTPILKAQHPDYE\n+IFQLGIHAQRGVSCSDCHMPYKTEGGVKYTDHHISSPLRNVNASCQVCHR\n+QPEEELIKNVYERQDYVFTLRNRLEKQLAKVHFQAKFLWDNGATEEQMKP\n+ILDLIRKSQWRWDFITASHGAAFHAPIESQKVLGDGMFYAMQAESDMNGL\n+TDKLKITAKFEMPDISTKAKAQAIIGLDMEKEEANKKQFMKTIVPKWIKE\n+AKEKGNLVTQK-------\n+>888059.HMPREF9071_0710\n+-------MM-----MKKKHWLIAGILAIVTFLLGLLASSIMNRSTEA-KI\n+IAKEGNNLAD-QECRNELYAPFYPREYDSWAATADTTFHSKYMSSQDDDM\n+LEQRPEMVILWAGYAFSKEYNAPRGHMHAIEDVTKILRTGAPTD-STHSP\n+QPGTCWTCKSPDVPRLMKKVGLEAYYSAPWDKWGSEIVNPIGCATCHNTK\n+TMSLAISQPALVEAFARQGRDINKATHQEMRSLVCAQCHVEYYFKG-D--\n+---KKYLTFPWDEGKAVEDMEKYYDESGWTDYVHKISRTPIIKAQHPDFE\n+ISQFGIHAQRGVSCADCHMPYKTDGAVKFSDHQISSPLRNVTASCQTCHR\n+QSEKELVKNVEDRQNAVFSLRNRLEKQLAKDHFKAKFLWDNGATEEQMKP\n+ILALLRKSQWRWDYITASHGAAFHAPVEAMRVLSDGMTFAMQAETDMDNL\n+TNKLNIKAAFVMPDISTKAKAQKEIGLDMEKEKAAKKRFLETIVPKWIEE\n+AKKEGRLVTQK-------\n+>553178.CAPGI0001_1715\n+--------------MKKRNWLLVGILAIVTFLLGLLANSIMNRSHEA-EF\n+IAKGGNNLED-QECRNELYAQFYPRQYDSWEATADTTFQSKYMSSQDDDL\n+LALRPEMVILWAGYAFSKEYNAPRGHMHAIEDVTKILRTGAPTD-STHSP\n+QPGTCWTCKSPDVPRLMKKVGLEEYYSAPWDKWGSEIVNPIGCATCHNTK\n+TMKLEVHQPALAEAFARQGKDINKATHQEMRSLVCAQCHVEYYFKG-D--\n+---KKYLTFPWDEGMTVEKMEEYYDKEGWTDYVHKVSRAPIIKAQHPDYE\n+LSQLGIHGQRGVSCADCHMPYKTDGAVKFSDHQISSPLRNISASCQTCHR\n+QSEEELRKNVYDRQDAVYGMRIKLEKELAKVHFKAKFLWDNGATEEQMKP\n+TLALIRKSQWRWDMVHSSHGAAFHAPIESERLLSDGLIYALEAEKNLDVL\n+KEKLHIAAEFVMPDISTKAKAQKEIGLDIPKEEAAKKQFLKTIVPKWIEE\n+AKKEGRLVTQK-------\n+>706436.HMPREF9074_03226\n+--------------MKKKHWLIAGILAIVTFLLGLLANSIMNRSQEA-EF\n+IAKGGNNLPD-QECKNELFAPFYPRQYDSWRATADTTFRSRYMSSQDDDL\n+LALRPEMVVLWAGYAFSKEYNAPRGHMHAIEDVTKILRTGAPTD-STHSP\n+QPGTCWTCKSPDVPRLMKKVGLDNYYSAPWDKWGNEIVNPIGCATCHNTK\n+TMKLEIHQPALVEAFERQGKDINNATHQEMRSLVCAQCHVEYYFKG-D--\n+---KKHLTFPWDKGMTIEKMEEYYDAEGWTDYVHSLSRTPILKAQHPDYE\n+LSQLGIHGQRGVSCADCHMPYKTDGAVKFSDHHISSPLRNVSASCQTCHR\n+QSEEELVKNVYDRQDAVYGMRMKLEKQLAKVHFKAKFLWDNGANEEQMKP\n+TLALIRKSQWRWDMVHSSHGAAFHAPIESERLLSDGLIYAYQAENNLDVL\n+KEKLNIKTAFVMPDISTKAKAQKEIGLDIPKEEAAKKKFLETIVPKWIEE\n+AKKAGRLVSQK-------\n+>553177.CAPSP0001_1095\n+--------------MKKKHWLIAGLLAVVTFLLGLLANSIMNRSTEA-QF\n+IARGGNNLPD-QECKNELFEPFYPREYASWAATADTTFRSRYMSSQDDDL\n+LALRPEMVILWAGYAFSKEYNAPRGHMHAIEDVTKILRTGAPTD-STHSP\n+QPGTCWTCKSPDVPRLMKEVGAETYYSAPWDQWGSQIVNPIGCATCHDTK\n+TMKLQVKQLALQEAFKRQGRDINKATHQEMRSLVCAQCHVEYYFKG-D--\n+---KKYLTFPWDEGMTVEKMEEYYDKEGWTDYVHSLSRTPILKAQHPDYE\n+LSQLGIHGQRGVSCADCHMPYKTDGAVKFSDHQISSPLRNVSASCQTCHR\n+QSEEELVKNVYDRQDAVYGMRMKLEKQLAKVHFKAKFLWDNGATEEQMKP\n+TLALIRKSQWRWDMVHSSHGAAFHAPIESERLLSDGLIYAYQAENNLDVL\n+KEKLNIKTAFVMPDISTKAKAQKEIGLDIPKEEAAKKKFLETIVPKWIKE\n+AKEKGRLVTQK-------\n+>521097.Coch_1101\n+--------------MKKKHWLIAGLLAVVTFLLGLLANSIMNRSTEA-QL\n+IARGGNNIKE-GECRNELYEPFYPREYASWAATADTTFRSKYMSSHDDDL\n+LALRPEMVILWAGYAFSKEYNAPRGHMHAIEDVTKILRTGAPTD-STHSP\n+QPGTCWTCKSPDVPRLIKEVGAETYYSAPWDQWGSQIVNPIGCATCHDTK\n+TMKLQVSQLALQEAFKRQGRDINKATHQEMRSLVCAQCHVEYYFKG-D--\n+---KKYLTFPWDKGMTVEKMEEYYDAEGWTDYVHPLSRTPILKAQHPDYE\n+LSQLGIHGQRGVSCADCHMPYKTDGAVKFTDHQISSPLRNVSASCQTCHR\n+QSEEELVKNVYDRQDAVYGMRMKLEKQLAKVHFKAKFLWDNGATEEQMKP\n+TLALIRKSQWRWDMVHSSHGAAFHAPIESERLLSDGLIYAYQAENNLDVL\n+KEKLNIKTAFVMPDISTKAKAQKEIGLDIPKEEAAKKRFLETIVPKWIKE\n+AKEKGRLVTQK-------\n+>873517.HMPREF1977_1975\n+--------------MKKKH'..b'AKYVGLDMKTLHAQKQDFLNTVVPKWIET\n+ARKNKRFITKPM------\n+>626522.GCWU000325_00563\n+---M----AK--QLKKWQGWLLFGGAMVIVFVLGLICSSLLERRAEVASI\n+FNNRRIQMTDSIVSQNEKFAEDFPREYQSWAMTADTTFESKYNGSQEKDV\n+LEEHPEMVILWNGYAFSKEYNTPRGHRHSVEDLLKILRTGSPGVDGQTDI\n+QPGTCWTCKGPDVPRLMREQGTDKFYAAKWSDWGDQVMNTVGCSDCHDAR\n+TMELRPARPALYEAWARVGKDVRKASHNEMRSLVCAQCHTEYYFEKE---\n+--NGNYLHFPQERGLLCEDAEAHYDSIGFYDYINPLSKAKILKAQHPGYE\n+LFMQGIHGQRGVSCADCHMPYISEGGVKYTDHHIMSPLAHIDRTCQTCHR\n+QDAETLRQNVYERQQKVYDFRKRVEKELAYAHIEAKFAWDKGATEAEMKE\n+VLSDLRKGQWRWDYAVASHGAAFHAPQEVMRLLAGAMEYAKDARLQIARV\n+VAKHGYTGTIPIPDISTRDKAAKYCGLDMAKLRQQKKQFLDTVVPKWVET\n+ARKNKRFITKPI------\n+>553174.HMPREF0659_A5771\n+---M----AK--TLKKWQGWLLFGGAMVLVFILGLLCSSMLERRAEIVSV\n+FNNRRTPMTDSIVSQNEKFAADFPREYETWAMTEDTSFVSKYNSSQEVDV\n+LAERPEMVILWAGYSFSRGYNTPRGHRHCIDDLRKIMRTGSPGVDGQDDI\n+QPGTCWTCKGPDVPRLMREKGTDKFYAAKWSDWGPEVMNTVGCSDCHDAR\n+TMELRPARPALYEAWARVGKDVRKASHQEMRSLVCAQCHTEYYFEKE---\n+--NGNYLHFPQEKGMTCEAAEEYYDSIGFYDYINPLSKAKILKAQHPGYE\n+LYLQGIHGQRGVSCADCHMPYISEGGVKYTDHHITSPLANISRTCQTCHR\n+QDAETLRQNVYERQQKIYDFRTHVERELAAAHIEAKFAWEKGATEAEMEP\n+VLKDLRKGQWRWDYAVASHGAAFHAPQEVMRLLGSAMEYAKDARLQIARV\n+VARHGFTGQIPLPDVSTKAKAQSYIGLDMTKLNAQKKQFLDTIVPKWIEQ\n+ARKNKRFITKPM------\n+>649761.HMPREF0973_00386\n+---M----AK--TLKKWQGWLLFGGAMVIVFFLGLLCSSMLERRAEIASV\n+FNNRRTQMTDSIVAQNEKFAEDFPREYETWAMTEDTSFVSKYNSSQEVDV\n+LGQRPEMVILWAGYSFSRGYNTPRGHRHCVEDLRKIMRTGSPGVDGQDDM\n+QPGTCWTCKGPDVPRLMREKGTDKFYAAKWSNWGPEVMNTVGCSDCHDAR\n+TMELRPARPALYEAWARVGKDVKKATHQEMRSLVCAQCHTEYYFEKD---\n+--NGNYLHFPQEKGMTCEAAEEYYDSIGFYDYINPLSKAKILKAQHPGYE\n+LYLQGIHGQRGVSCADCHMPYISEGGVKYTDHHVMSPLAHIDRTCQTCHR\n+QDAETLRQNVYERQQKIYDFRTHVEKELAAAHIEAKFAWDKGATEAEMQP\n+VLTDLRKGQWRWDYAVASHGAAFHAPQEVMRLLASAMEFAKDARLQIARV\n+VARHGFTGQIPLPDISTKAKAQSYIGLDMPKINSQKKQFLDTIVPKWIET\n+AKKNKRFITKPM------\n+>888743.HMPREF9141_0857\n+---M----AK--TLKKWQGWLLFGGAMVIVFVLGLLCSSMLERRAEVASI\n+FNNRRTQMTDSIVSQNEKFAEDFPREYETWAMTEDTSFVSKYNSSQEVDV\n+LAQRPEMVVLWAGYAFSREYNTPRGHRHAIEDLRKILRTGSPGVDGQEDI\n+QPGTCWTCKGPDIPRLMREKGTDKFYAAKWSDWGPEAMNTIGCSDCHDAR\n+TMDLRPARPALYEAWARVGKDVKKATHQEMRSLVCAQCHTEYYFEKE---\n+--NGNYLHFPQEKGLTCEAAEEYYDSIGFYDYINPLSKAKILKAQHPGYE\n+LYMQGIHGQRGVSCADCHMPYISEGGVKYTDHHVMSPLAHIDRTCQTCHR\n+QDAETLRQNVYERQQKIYDFRTHVEKELAAAHIEAKFAWEKGATEAEMKT\n+ALSDIRKGQWRWDYAVASHGAAFHAPQEIMRLLASAMEYAKDARLQIARV\n+VARHGFTGQIPLPDLSTKAKAQSYIGLDMPKLNKQKKQFLDTVVPKWIET\n+AKKNKRFITKPM------\n+>767031.HMPREF9137_1264\n+---M----AK--TLKKWQGWLLFGGAMVIVFVLGLLCSSMLERRAEVASI\n+FNNRRTQMTDSIVAQNEKFAEDFPREYQTWAMTEDTSFVSKYNSSQEVDV\n+LAQRPEMVILWAGYSFSRDYNTPRGHHHCIEDLRKILRTGSPGVDGQKDI\n+QPGTCWTCKGPDVPRLMREKGTDKFYAAKWSDWGPEVMNTIGCSDCHDAR\n+TMDLRPARPALYEAWARVGKDVKKATHQEMRSLVCAQCHTEYYFEKE---\n+--NGNYLHFPQEKGMTCEAAEEYYDSIGFYDYINPLSKAKILKAQHPGYE\n+LYLQGIHGQRGVSCADCHMPYISEGGVKYTDHHVMSPLAHIDRTCQTCHR\n+QDAETLRQNVYERQQKIYDFRTHVEKELAAAHIEAKFAWDKGATEAEMQT\n+ALSDLRKGQWRWDYAVASHGAAFHAPQEVMRLLASAMEYAKDARLQIARV\n+VARHGFTGQIPLPDISTKAKAQSYIGLDMPKLKKQKKQFLDTIVPKWIET\n+ARKNKRFITKPM------\n+>643867.Ftrac_2736\n+----------------MKNWILFGITAIAVFLLAMLAYTIIDRKAEA-RF\n+AYQPKVEIQS-IEPRDSVWGLNYPRQYQSYMKTADTTFKSMYNTSGFADI\n+LDEQSELVVLWAGYGFGKDYNQPRGHVYAVADILKTLRTGAPMK-QGDGP\n+MPSTCWTCKSPDVPRLMKEMGATEFYSKQFSDLGSEVINPIGCADCHDPN\n+TMNLTVTRPALIEAYEAMGKNINDASHQEMRSLVCAQCHVEYYFDKDKPG\n+KEGANYLTFPWKDGMDVESAEAYYDKTDFADWVHPISKTRMLKAQHPDYE\n+LFQQGVHAKRGVSCADCHMPYKSEGGQKFTDHHIGSPLENVENSCFVCHR\n+EKVSDLVSDVYERQRKIKEGTSKLQTLIAKAHIEAGKAWELGATEEQMKE\n+IQKGIRHAQWRWDYSVASHGAAFHAPLETSRIVTSATRIIMESRLKLMQL\n+LNSLGHSGDVEMPNLNSKEALQEYTGIDIKKERYNKEKFLEEIVPKWMKE\n+GKEREAKMNVKEVGSK--\n+>1046627.BZARG_2685\n+------------------------MTIVVVFLLGLLASSIINRKSEA-KY\n+KYVPNVQIGE-NEPRNEEWGKNYPREYQSYLQTADTSFTSYQGGSSSIDM\n+LEEDPRMVVLWAGYAFSKDYNQGRGHFYAIDDLQNSLRSGAPES-KEDGP\n+MPATCWACKGPDVPRLMDEHGVGEFYSGTWAENVSEVVNPIGCADCHDPT\n+NMKLLITRPALVEAFQAMGKDINKSTHQEMRSLVCAQCHVEYYFNTKKEG\n+HEGTPYLTFPWENGFAVEDMEKYYDDIGFSDWTHAISKAPMLKAQHPDYE\n+IFLTGVHADRGVSCADCHMPYKSEGGQKFTDHHLQSPLNNVANSCQVCHR\n+EETDKLITNVYDRQRKANENRIKLEDVLVKAHVEAGKAWELGATNEQMKD\n+ILMSIRHAQWRWDYTAASHGASFHSPVEIGRVLGSGLAEAQEARVMLVRL\n+LANLGHNDPVAMPDISTKAKAQKYIGLDMEKLREEKEAFKTNVLPKWLEE\n+AKQREAKMDSKKVVSTDN\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,480 @@\n+>755732.Fluta_1318\n+-MMKK-Y--------------G-IIAILILVIAAFVIVPLLKEN-GGETE\n+---D-T---------------LMAKFDLP--GSLIQVKYGQNTPIKFRIP\n+EGLVKVELIYNDSIFETWNNP-KEQIRTV--AMQTNYYG-VGTRPLVLRS\n+TFQD-QTVLENSCNIRVVSDIVPEKLLAKIVKEYPHSKENYTQGFEFDGN\n+QLYEGTGDP-----GQ----L-GKTLVGP-VSLQTGTFSEPKNGLDA-TY\n+FGEGITVLGDLVYQVTWQNSRCFFYDKKTMQLKGDFNY---VGQGWGLCN\n+DG-KSIIMSDGSERITFRDPKSFQA-TKFIEVYDNLGPRTQLNELEYIDG\n+KIYANVYT--TSIVLVIEPTTGRVLEEIDASELVLRG--K------NG--\n+--GDVLNGIAHNKLSNKTYMTGKYWTKTFEVQFQK-----\n+>926562.Oweho_1339\n+--MRK------------------IV-FLSVIILVQGAC--QQ----SATS\n+---L-----------------VAVSSNLDS-YANTRLHWGDPVSIEMETT\n+N----HDSIQLQLNGKKVAAS--N----V--TLGKENSV-LGKNTLKLTV\n+FTGA-EN-TVREVSLLIVSSQKPQRKSYSIINTYKHDASYFTEGFYYEDG\n+MLYEGTG--------L----N-GKSKLVT-YNLASAKIEN-SMDLDA-QF\n+FGEGIAVVGDSIFQLTYKAQKAFIYNRTTFEKVGEFNVP-FSAEGWGLCY\n+DG-KSLIMSNGSHFVYYINPKDFTY-TGSLQVVDDKGIHGKLNELEYHNG\n+KIYANVWY--EKEIVVINSQTGAVEEVISLDNIPSKNFQQ----------\n+---GVANGIAI--IDGNLLITGKNWTETYELQVNDL----\n+>700598.Niako_4408\n+------------------MKKV-LFA-AIVILTALAAC--N---------\n+--------------------------------------------------\n+--------------------------------------------------\n+-DHTDAGT-NNTGETNNNANAAPPVIQYAVVNKYPHDTAYFTEGLEFHNG\n+QLFESSG--------GNADESPYPSELGI-ADLKTGKVTSK-VKLDKTKY\n+FGEGITFFGDKLYHLTWTSGTGFVYDANTFKLIKEFKI-P-AKEGWGLTH\n+DS-THLIMSDGSSNLYYLTPDSLKI-ANILRVTDNNGPITNINELEYVNG\n+FIYANQWE--TNYILKIDPGTGSVVGKINLENLQKEAA-S----LRPG--\n+--ADVLNGIAYNKETNQFLVTGKRWPFLYEIKVQ------\n+>700598.Niako_2739\n+------------------MKTF--LL-SLLTVLVLSGC--G---------\n+--------------------------------------------------\n+--------------------------------------------------\n+---SS----EEKEEEKTTAPVTPAI-KYEEVDYFMHDTSLFTEGLLIHDG\n+QLFESTG--------SPE--KG-RKSLIGINDLKTGNFIKK-VELGQDSL\n+FGEGIVFFKNKLYQLTYKNHIGFIYDANSYKKIGQFPI---KKEGWGLTT\n+DG-KAIVMSDGTDTLNYLNPDDLTT-YKKLPVTENGRRRDSLNELEYIKG\n+YIYANIWL--TNNIVKINPADGKVVGKLDLSTLALKAA------LTTG--\n+--GDALNGIAWDSTTGYMYVTGKLWPHIHQLKLK------\n+>709991.Odosp_2896\n+--MGT-GRKLNRYE----QRMT-CFF-YILCAFFICSC--G---G-NKTA\n+NKEK-KTPLAAELPKDEVRYVKSIQLTS-P-GKDKMYAFNEEIVIGFESK\n+D-RFPVDSAAFYIDGQQIATAGK-EDRSF--TYRIPEGK-TGNMTIKVMA\n+WHPDNKRG-IATTTIRVKPDQAPAIYSYEVVNVFPHDPKAYTQGLIYQDG\n+FIYEGTG--------Q----Y-GESSIRK-TDMQTGKTLSV-LNID-SQL\n+FGEGITIYEDKIYQITWRSRKGFIYDLKTFTLESTFNY---NSEGWGITT\n+AG-DHLIMSDGSNKLYHIAPSTFNI-LKEVEVYDHNGPVDQLNELEYVDG\n+MIWANVWL--TDRIVVIDPETGIVRGELNLPGLLPAAD-KA--RLDDK--\n+--DDVLNGIAWNAGKGTFYVTGKRWPKLFEIKVKLIPYGR\n+>762903.Pedsa_2683\n+--MLF-GTIKKQTLN------S-LF-IAPLIALTAFSC-----K-ES---\n+---HK----------------KSESIAL-FPESGSTYKLGDEFKAFVKTA\n+N---LPDSVQYYVDGKLIETK-K-DTSNI--NINTSNLS-LGTRIISAKV\n+FSEG-KEE-EIQSNITILTPRVPKQFGFNVVKTYKHDTSSYTQGLEYHDG\n+IFYESDG--------E----Y-GASSLRK-VSVE-GKVLKQ-IDLDK-RY\n+FAEGITIIGDKILMLTYKEKVMFEYDKNTFELLRTIPYN-HAEEGWGLTF\n+DG-NVIYNTDGTNRIFKLNKDTYQP-EGFIEVYDNKGPVNYLNEMEWIDG\n+KIYANIYT--SDLIAIIDPKTGEVEAYINLSGIRKGSV------EDES--\n+--QDVLNGIAWDAKGKRLFVTGKKWSELYQITLKEH----\n+>714943.Mucpa_2667\n+--MKY----------------R-II-AVALITTTVAGC-----F-TK---\n+----K----------------QSAVLSV-SPEAGTSYKLGDQIPVSVSVP\n+T-DTKADSVQYLVDSVRVLSR-K-DTLSI--KIKTDSMK-LGSKLITARV\n+FSGG-KPA-EVSTNVMLLAPKAPAVYTFKIEKVFPHDTSSYTEGLQYVDG\n+FLYESAG--------N----Y-GNSSLRK-VDLNTGTVVQK-AKMDP-MY\n+FGEGIAVVGDKIIQLTYKEKKGFVYDKNTFKILSTFNFN-WAPEGWGMTY\n+DG-KNLLHNDSTNRIWLLNKDTYMP-QGYLDVYDDKGPVNQINEMEYIDG\n+KIYANIYT--TDTIIVIDPKNGAVVESVDLKNLYPMDSRPYSVKSDPA--\n+--NNVLNGIAWDEKGKRLFVTGKKWDKLFQVKFVKQ----\n+>743722.Sph21_0668\n+--MSY-TLHLLYLCM----N-K-FLLLALTALCSVAAC-----D-REKSN\n+N--SSN---------------KSLSFSA-V-EPGSLINKGDSVSLQLSLP\n+A-DLSFDSIAYSLNDKPYVTV-K-DSGAV--WLKTDSLG-MGSQLITANV\n+FKAG-QSE-SASTNIVVVASKLPEQYSFTVVNTYPHDAHAYTQGLEYHDG\n+FLYESTG--------Q----R-GQSTLRK-VELKTGKVVKK-IDLPS-KY\n+FGEGMTFVGDKIVQLTWEEGVGFVYDRNSFEKVGEFPYQ-ASKEGWGLCF\n+DG-QRLIKSDGSNRLYFLNKDNFKE-EGFIEVYNHKGPVDKLNELEYIDG\n+KIYANVYY--SDVVVVIDPHSGQVEAEINLIGLLPQKDV------TED--\n+--TNVLNGIAYDQQGKHLYVTGKNWDKLFEIKLLGR----\n+>525373.HMPREF0766_10660\n+--MKK------II------------GVFAVGAMLLSSC-----F-T----\n+----KK---------------GKLEFVS-P-ESGKVVILGQKVNLKLNFA\n+S--AALDSVVYSVDGNIIGRK-Q-DT'..b'DTLEKLGNFAYG-ESREGWGLCN\n+NG-EYLFKSDGSQRIWKLDPRTLEE-VGYIETVTDKSVFNKANELEYVNG\n+KIYANVWQ--RPSMMIIDAASGAIEGVVNFGGLENKVTQH------DQ--\n+--LDVFNGVAYHGGRQTFFVTGKRWDKLFEVRIVKRDP--\n+>867900.Celly_2663\n+--MKT-L--------------K-FLT-YSAITILLISC-----G-GANTP\n+---A-S---------------KLFEIQI-T-GKKAKFHQNETVDITVKNK\n+K-NKTINAVSYTLDGEKVDVK-D-N------KLVLKTEK-VGKKTVTAEI\n+TYDDDTVV-EVSKKITVFASTAPSIYTYEILNEYPHNPNYFTQGLEFYKD\n+TLYESTG--------K----R-GKSVLVK-LDYKTGTIFKE-HKLKD-TQ\n+FGEGITILDNKIYHLTWQSNIGFVYNADTFKEIDQFTYG-KSKEGWGFCN\n+DG-EKLYKSDGSEKIWTLNAETLIE-ESAIEVYTNSKKLIKINELEYVDG\n+KIYANTWQSGQDVAVIINPNSGIVEGIINFNGLKDKVTKT------DN--\n+--VDVLNGIAYNPTTKTFFVTGKNWDKMFEVALIKK----\n+>886377.Murru_3418\n+--MGK-L-----------------FS-ITGVLLFFLGC-----G-GNA-D\n+---P-A---------------KHFSIQL-E---NKNIQQNQQVGVTLKNK\n+K-DIEISDLRYYMDGKELLVE-N-G------KLTLDLPT-LGNKTLVAKF\n+NIEEQ-AV-EVEKKLRLLAAAAPEVYTYEIINSYPHDTGAYTQGLEFYKG\n+TLYESTG--------K----R-GASTVRK-VNFETGEVVTN-IPMDD-SV\n+FGEGITIMNDKLYQLTWQSGMGYVYDISNLEKIKNFTYG-KSREGWGLCN\n+DG-KKIFKSDGTEKIWFLDPETLEE-QGHIEIVTNKSIFNSANELEYVAG\n+KIYANVYQ--KESMMIIDATSGAIEGVINFGGLKNKVSKG------PEWD\n+EGNSVLNGVAYHPERETFFVTGKNWDKLFEVKIRKKD---\n+>688270.Celal_3685\n+--MKS-I--------------F-SIT-SLLLIIILNAC-----G-SSNAV\n+---P-A---------------DLFEIQL-T-GNKTEFQQNEAVGISLKNK\n+K-GLEVESILYSINDQPLKVE-N-D------QIVFDMPH-LGEKTITATI\n+AYEGK-TG-NIQKNIKILAAKGPEVYTYEIINEYPHDQKAFTQGLEFYKD\n+TLYESTG--------R----K-GQSFLRK-LDFKTGKVFKQ-ADLDK-QY\n+FGEGLTILNDKIYMLTWQSGLGFIYDVNTLEKIDSFKYG-ASKEGWGLTN\n+DG-ERLYKSDGSEKIWLLNPETLVE-EDHIETVTNKSIFNKTNELEYVDG\n+LIYANVWQ--KESMMIIDAVSGAIIGVINFGGLKDKVTKH------AD--\n+--LDVLNGVAYNPKRGTFFVTGKNWDKLFEVKIIKK----\n+>313603.FB2170_13191\n+--MNP-F--------------K-VLV-FNFFLLFFVAC-----G-SGNTS\n+---A-S---------------SLFEIQL-E-GNKTSFKQNQSVGIAIKNK\n+K-EKSIDKIIYTIDGKELQLS-G-N------KIALDLTT-LGNKILKATI\n+GYEDT-TA-EISKKIKVLAPTAPALYTYEIINEYPHDIKAYTQGLEFHDG\n+ILYESTG--------K----K-GRSSLRK-VDYNTGKVLAQ-IDLEN-TQ\n+FGEGITIMNGKIYQLTWQNGIGFIYDLTDFKKIDSFQYG-QSKEGWGLCH\n+DG-EKIFKSDGTEKIWFLNPDTLAE-EGFIQTVTNKSVFNMANELEYIDG\n+KIYANVYQ--KPSMMIIDALSGAIEGVINFGGLKEKVTKH------AD--\n+--LDVLNGVAYHPERKTFFVTGKNWDKMFEVNIIKK----\n+>865938.Weevi_0796\n+------------------MKRF-YIL-FGLLVLSVTAC--K---D-DASV\n+---N-N---------------PLITQQV-SAIEEKHYKIGDSLEITLEGL\n+T---NITEVKVEIDGKDFPNPG---------KITLENVG-LGQHNVNVKF\n+FNGSELTA-TREFNILVFADHPAQEWQYNLVNTYPHNPADFTQGFYYKDG\n+FIFEGTG--------L----T-GQSRLVK-YRLGSTTEELT-GEVE-KTS\n+FGEGITELNGVIYQLTWQNRLIYEYDQN-FELIRKITMPGEIREGWGITT\n+MG-QELVITDGSQKIHFFDKD-FNY-KRTIQAVDDKQAYSNLNELEYHNG\n+LLYINIYQ--QNIIVAVDPASGAVVGKMNLEAFKA-EQ-A------AD--\n+--ADVLNGIAF--KGENMLVTGKLWNKIYEVSIKR-----\n+>531844.FIC_01534\n+--MSI------F-EKNLHMTIR-TFI-ALLAFMFVLSC--N---K-DKEI\n+---L-N---------------TLNDYNL-S-MENKGYHFGDAIELPKDVA\n+D---NAESITISFGDKETSK-L---------IVDPAFFT-LGDNAVTFNI\n+KKKNGEII-SQDATINVFAKNPEAELKYDIVKEYPHDSANFVQGFLIEGN\n+TIYESDG--------Q----K-GSSRIIK-YNLGSTTPIAA-TPQP-AEI\n+FSEGAAIIGDKIYQLTWLHKKGFIYNKSDLSLIGEFAYPNVVGEGWGLTY\n+DG-KNLILSDGTKNIYFLNPANPSEIVRYISVAGHTEAFDKLNELEYHRG\n+FIYANVWQ--KPVILKINPANGEVVGKFDFSEIAKLHT-T------NE--\n+--DDVLNGIAF--KGENMLVTGKNWDKIYEVAIK------\n+>992406.RIA_0005\n+------------------MKKN-IIV-ACLGLMLLASC--N---K-DKEI\n+---L-N---------------TLNEYNL-S-MEEKGYHFGDAIKLPEEVT\n+K---NAETISISFGDKEISD-L---------KVTPEVFS-LGDNEVSFVI\n+KTKSGETL-TQDATIYVFAKNPEQNLSYTIVNEYPHSTENFVQGFQLEGN\n+TIYESDG--------Q----N-GSSRILK-YNLGSVTPLAV-TPQS-NEI\n+FSEGSTIVGDKVYQLTWQNKKGFIYDKASLKLLSEFPYPGAIGEGWGLTY\n+DG-KNLILSDGTKNLYFLNPNNPSEITKQIAVAGNTQAYDRLNELEYHQG\n+FIYANVWQ--QPYILKINPNTGEVVGKFDFSEIAKKHT-A------GE--\n+--DDVLNGIAF--KGENMLVTGKNWDKIYEVKIK------\n+>525257.HMPREF0204_12769\n+------------------MKKN-IIA-GFAAILLLASC--N---K-DKEI\n+---L-N---------------TLNTYNT-S-MEAKGYHFGDKLELPKEVT\n+E---NAESVTISFGDKETTN-L---------TIDPKFFT-LGDNAVTFNI\n+KTKGGEVL-NQDATINVFAKNPEKNIPYQIVAEYPHDPKNFVQGFQIEGN\n+TIYESDG--------Q----N-GSSQILK-YTLGTTTPLAS-TKQA-QED\n+FSEGSTIVGDKVYQLTWQSKKGYIYDKSSLKLLSEFAYPNVLGEGWGLTY\n+DG-KNLIASDGSKLLYFLDANDPSKLIKYIAVAGSSQAYDQLNELEYHNG\n+FIYANVWQ--KPIILKINPANGEVVGTFDFTEIAKQNT-K------GS--\n+--DDVLNGIAF--KGDNMLVTGKNWPKIYEVVIK------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,350 @@\n+>865938.Weevi_1053\n+MPL------------------------IN-RSTY-RPKKIYQQEAHLSTI\n+IPARLKKHPIPNYTRKKLELDDGDFLNLDWRKKE--------------KS\n+------------------------N----KIVILCHGLEGDSKRTYLNSC\n+SDYFYERDFSVLAWNYRSCGGEMNRLKRLYHHGAYDDLERVVNHLIS--L\n+GYTEIALVGFSMGGALLMNYLGNV--SVPKEVKVGVGISVPISLKSSADR\n+LKAFPNVVYFQNFKRTLLPKIIEKAKQFPG--A-INLDLLKKVRSFDQID\n+DYVTAPLHNYPNKEAYYTEASPKHCLHKIRTPCLVVNAKNDPFLGKECYD\n+VSLFENHPFVYFEQPEFGGHCGFSLSG--Q--R-HSWADKRAYNFVMKYI\n+RKTEN--S\n+>376686.Fjoh_4611\n+MPL------------------------IE-QSEY-TFPSIIHRNRHVSTI\n+YAALFKKFEVPEYTREKHELNDGDFINIDFVLND--------------SK\n+-----------------------------KAVILCHGLEGDSRRTYNNSC\n+AAYFLQKEFSVFAWNNRTCGGEMNRLPRLYHHGAVDDLDEVVQFVLR--K\n+GFDDVYLIGYSMGGVQLLNYFGWT--KIDKRIKAGVSISVPTHIATSAAV\n+LKQGFNRVYLKNFTIDIKRKLKYKAAQFPD--F-INRDQIDKISSFDEVD\n+HYFTAPLHGFASREDYYQRVSPEFSLKNITTPVLIINSLDDPFLGERCYP\n+RAIAQDSEYVYLETPKYGGHCAFPLRD--S--M-YSYAEKRAYDFFESRE\n+KNAQIIKA\n+>313594.PI23P_11652\n+MP-------------------------LI-DSDF-TPTL-PFKNTYFNTM\n+YRPFFMK-DECAYKRKRITTWDQDFIDLDFSIVG----------------\n+------------------------A---KTLALLIHGLEGSAASKYMTAT\n+SNHLNQNGLDTVCLNLRSCSGEDNLQLSTYHSGKTEDVDFVIQHLLEN-Y\n+SYENIVIVGFSLGGNLTLKYLGEYREKLSPKIKGAVAVSVPIDITTAEKE\n+MDKLKNKVYVEVFFKTLKNKILEKAFKFPE--YRLDKEKLFRATKFKHLE\n+LLYTVPVFGFKSPEDYWKKASSKPYLSKIDRPTLLINAKDDTFLSPECYP\n+IKEAMQSASFYLETPEYGGHVGFITSF--KN-HENSWLEKRITQFIKEHI\n+LI------\n+>313598.MED152_02475\n+MP-------------------------IL-PSNF-SPTI-PFRNGHFNTM\n+YRPLFMK-GVVNYKRERLHTWDNDFLDLDFSKVG----------------\n+------------------------S---KTLAVLIHGLEGSSSSHYITAT\n+IKHLNNKNLDAVCINLRGCSGEDNNLLATYHSGKTEDVSFVMNHLLDK-Y\n+SYENIVIIGFSLGGNLTLKYLGEQGKELPSEIKGGIACSVPVDIASAEKE\n+MDKLKNKLYMEVFFKTMKNKILEKAHKFPE--YKLDKDKLFKATKFKHLE\n+HLYTVPVFGFESPEDYWQKASSKPYIPSINRPALLINAKDDTFLSKECYP\n+KEEAKTSDNFFLEITKYGGHCGFMSSF--KP-SDNTWLEERIAKFIQRNI\n+NIDMP---\n+>649349.Lbys_2766\n+MQNL------------------------V---KI-RPPF-LQWGGHLQSI\n+YPSLFRAVP-IVYERERLELEDGDFLDLDWHKV--------------GSK\n+-----------------------------KLIIVTHGLEGDSTRPYVTAL\n+IKLFSQQGIDGLGWNCRSCSGEINRLPRFYHHGDAEDLRTVVEHAIR--L\n+GYDSIFLSGCSMGGSLTLRLLGEHPERLPKEVMGAFVGSVPLDIYSSVRE\n+LDRPYKRFYMNRFLRKLKAKLMIKEQMFPGNEL-VSCRDFVHIKNFVDFD\n+GRYTAPIHGYRSAFDFYEKASTKPLLHRVQVPTMIVQSLNDPFLGPECYE\n+---PSDNPLIQFILTKNGGHVGFMVQG--QE---YTWTEKKALEFFQSLL\n+--------\n+>760192.Halhy_4642\n+MP-L-----------------------VP-HSSYPGPPR-YQWNGHFQTI\n+LPALTRKIKAVHYERERLELSDGDFVDLDWLDA--------------ESQ\n+-----------------------------TLVILSHGLEGSTDRVYMKAA\n+AKYFHEHGWDVLGWNCRSCSGEMNRLLRLYNHGEIGDFGQVIDHALQ-RK\n+NYTKIHLIGYSMGGSILLKYLGVHGKNIPEPIKTGIAFSSPCDLPDSIQT\n+LELPGNWFYRRKFFNSLRKKIIAKAAQFPGQ---IDLSKFEQIKSWRDFD\n+EFYSAPINGYKNAEDFYWQASAKNFVAGIQIPALLCNAQNDPILTPACSP\n+KELAKNHPYFHVETPHKGGHVGFAIKR--HP-GPYYWLEHRAMEFIKGQN\n+--------\n+>504472.Slin_5174\n+MP-L------------------------I-HSPYSGPPA-YQYNGHLQTI\n+IPSLTRAVTGISYERERLILTDGDFVDLDWVKQ--------------GQK\n+-----------------------------RLVILTHGLEGDSNRQYIRGT\n+AKLFAQHNYDVLAWNCRSCSGEMNQAFRLYNHGEIGDFGEVIDHALQ-TK\n+RYQELILVGYSMGGNITLKYLGVHGNQLSKAIKGGIAISAPTDLGASACL\n+LDRPSNRFYRNRFMKKLLVKISRKAQMYPGR---LDMSKVRQVKQWKDFD\n+EFFSAPVNNYRDADDFYTQASAVNFMPDIAVPTLLLNAQNDPLLSAECSP\n+EELAKAHPHIFLETPRTGGHVGFQLVR--DP---HTYAERRALWFAQRLT\n+NG------\n+>761193.Runsl_1609\n+MP-V-----------------------VR-QSTYPGPPR-YLFNGHLQTI\n+IPSVFRKIEGVAYERERFMLSDGDFVDLDWLDT--------------KSK\n+-----------------------------KLVVLTHGLEGDSGRHYIKGT\n+AKLFARHGWDVLAWNCRSCSGEMNKAFRLYNHGEIGDISELIDHALR-TK\n+HYEKIALVGYSMGGNISLKYVGVKGKDLPDAVQGVAAFSAPTNLKTSAEL\n+LDLPKNRLYRERFMKKLTKKITAKAELYPGK---LDMERLKNVKVWKDFD\n+DFFSAPVNGYRDADDFYEQASAVNFIKEVHIPVLICNAQNDPILNDDCAP\n+KALAEKHRHIFVETPKTGGHVGFLVKN--DE---FTWAERRALTFLS---\n+--------\n+>643867.Ftrac_0680\n+MP-V-----------------------IK-NSQY-KPPF-YLFNQHMETI\n+FPSALRKVKGVQYERERIETRDDDFLDIDWVKN--------------GNS\n+-----------------------------RLIIASHGLEGSSDRPYIMGI\n+AKLFSQNKWDVLAWNCRSCSGEMNRREFLYHHGFTQDVEEVVQKALK--E\n+GYKEIVMIGFSMGGSLTLKYVGENGKDLYPEIKGAMAVSVPCNLSSSSRM\n+LALKKNKFYQNRFMRKLDVKLREKNEQYPNL---IHIKPWQSFADFHEFD\n+THYSAKIFGYKDAQDFYDNVQCFPHLKKIAIPTLILNSLNDPMLTGDCYP\n+ESEAERNGNIELELTKHGGHVGFLQKG-'..b'215\n+MPL-------------------------V-ASTY-NPPI-LFKNGHLSTI\n+YSGIFRKVDGVAQERERITLFDTDFLDLDWSFA--------------SQ-\n+---------------------K--S---NKVMIILHGLEGSAQRPYIMGS\n+AKVFNQNGYDACAINLRSCSGAPNLLFRSYHSGATEDLDAVIQHILT-NK\n+SYDEIYIKGFSLGGNLALKYLGEKR-EIPKAVKGAVAVSVPCDLYSSLKQ\n+LLLPKNRLYAARFKKHLVEKLRVKQELFPN--E-ISDKDIASIKTLKDLD\n+DIYTSRAHGFTDAIDYYTKSSCLPFLPNIKIPTLIINSKNDSFLGPECYP\n+YTEAEENKNLFLETPNFGGHVGFYGVK--N----TTYTEKRCLNFLNEL-\n+--------\n+>309807.SRU_2232\n+MPTPTALHLRVPHPSTPTPRRPLANVPVR-PSSY-TAPT-GLDGGHRQTL\n+YASLVRRVDFEYDYRERIDTPDDDFLDLDWARPRAA--------------\n+---------------------S--S---DRAVILTHGLEGSAGRGYMRGM\n+ARAFVRRGWDACALNLRGCSGTPNRQVATYHSGKTDDLALVVHHVLD--H\n+GYTSVALIGFSLGGNLTLKYLGERGPQVDDRIRGAVALSAPVDLDASADR\n+IDRWSNWHYVQYFLRSLRHKMRVKADQHPA--R-VSIAPLSRIRSLREFD\n+DVYTAPLHGFDGAADYYRRASSRPSLSALAVPTLLLNAANDPFLPASCYP\n+YPIARPHDQLALEVPESGGHVGFVSFN--D--AGEYWSERRAASFLSPS-\n+--------\n+>504472.Slin_1075\n+MPL------------------------IA-PSSY-EPPT-RLWNGHLQTI\n+IPSLFRKVQ-VTYVRERIETPDDDFLDLDWSFSLGVRSEELEVRMANRTS\n+EPASATTDAQALLTPRSSLLAP--E---KPLVILSHGLEGSSGSSYLAGM\n+VRHLTKHGFDCLAWHYRSCSGELNRQQRFYHIGETGDLHFIIQHALS--K\n+GYQTIYLMGFSAGGNVTLKYIGEQGQLLHPSVKKAVVFSVPVHLMGSASR\n+LERWDSLVYNYRFNRTLKRKILQKASLMPG--V-FPTEAVAKARNIREFD\n+NLFTAPMNGFKDVTDYYTRSSSLQFIPTIAIPTLLVNAKNDPFLSPECFP\n+EALARELPNVWMEFPEEGGHCGFPSRK--EGIQGTYWSEERALHFLTITN\n+--------\n+>388413.ALPR1_15259\n+MPI------------------------IQ-NENY-QRPK-WLFNRHLETI\n+YPALFRTVNLQKPVRERITTDDKDFLDLDWYKQESP--------------\n+-----------------------------KLVIINHGLEGNSSRSYILGM\n+AKTFLENKFDVLAWNYRGCGDELNQTPIFYHSGATYDLNRVIEHAS---P\n+NYEEIYLVGFSLGGNLTLKYMGENGT-STEKIKKAVAISVPLHLSSSSQK\n+ISELENTLYSKRFLKTLKEKVQLKAKIHPN--D-IPVEMLRNVKTLAEFD\n+NYLTGPLHGFADAEEYYEVNSSLYFLDKINKPTLVLNAWNDPFLSKQCFP\n+VDLAKKLEKVYFEFPKNGGHVGFTNKI--P--KNPYYSEQRAVEFITQDI\n+--------\n+>880070.Cycma_0703\n+MPV------------------------VK-TSKY-LRNQ-LLFNGHLQTI\n+YPAIFRKKVVLPFERERISTSDGDFLDLDWLRNGKD--------------\n+-----------------------------TLVILSHGLEGNSQRPYMTGM\n+AKMFFESGYDVLNWNFRGCSESMNALPIFYHSGATYDLDLVISHAA---K\n+NYSNIHLIGFSLGANLTLKYLGETSWKSKIHIKKAVAISVPLDLGGSCDK\n+IDEFGNKLYAYNFLYSLKQKIRKKALHFPE--K-LSIDKLSNIHSLRDFD\n+NEFTAPLHGFKDATDYYQQCSSLYFLPQIKHPTLVLNAKNDPFLSRNCFP\n+TNAGKYKATLYLEYPKHGGHVGFSPRT--V--KERFWSETRALEFIQNEN\n+IN------\n+>471854.Dfer_4689\n+MPL------------------------VH-YSHQ-ISPF-WLPNGHFQSI\n+YPALFRQINGIKYFREKIVTPDDDFLNLDWSYAGNEV-------------\n+------------------------P---KPLIILSHGLEGNSTRQYITGM\n+VKLLTQNGFDCLAWNFRSCGGEMNQTARFYHSGATEDLNAVINYAFE--K\n+GYADVRLVGFSLGGNLTLKYLGEQGAAIDNRIKGAIVFSVPMDLKACSLA\n+IIEPRNQIYMHRFLKSLKPKVMEKAALYPQ--R-IDLKDHALVKTLYDFD\n+HIYTAPLHGFEGADHYYAECSSQFFVEPITVPTMIVNAENDPIVPFGSLP\n+IDVLRAHPNVTLLATRDGGHCGFRPAR--LTD-EFYWSEKYALGFLSGL-\n+--------\n+>761193.Runsl_2165\n+MPV------------------------LS-TNTH-RPPS-WLPNGHYQSI\n+YPALFRTVKP-AYQRERLTTPDDDFLDLDWSYAKTNEAKNSAN-------\n+---------------------A--S---PSLVILSHGLEGDSTRQYVTGM\n+VKLLNANGYDCLAWNYRSCSGEMNRQLRFYHSGETTDLEFVIQHALA--K\n+GYTELNLMGFSLGGNVTLKYVGEHGKNIHPAIKKAVAFSVPMDLLACSRN\n+IEKPENKLYLWRFLKSLKPKVAAKALQYPD--H-FDLNKWKQVKTFWDFD\n+HVYTGPLHGFEGADDYYEKSSSKNYIQHAAIPTLIVNAVNDPLVPYQSLP\n+ADVIADLPNVWLELTEAGGHCGFRPDR--FSQKGAYWSEMRALSFLNKA-\n+--------\n+>313606.M23134_04464\n+MP-I-----------------------IQ-SSSY-KAPA-WLPNRHWQTI\n+YPNVFRTVKGVNYQRERIQTPDDDFLDLDWSKT--------------GDK\n+H--------------------TTR-----SLVILSHGLEGAANRTYMLGM\n+AKAFNAQGWDALAWNLRGCSGEPNRTVKLYHHGITEDLDAVLKHVFA-HY\n+PYEKIALVGFSLGGNLNLKYLGEQGENLDSRIVKSVSFSTPCDLGSSAPL\n+LENRNNWIYQQHFKKKLVQKIKTKSKLFPKE---LPLELLKKVDSLLDFI\n+DIYLAPIHNFKNAEDYFNQVSACFFLDKIQIPSLIVNAINDSFLSPECSP\n+IAQAQNHPYVFVENPTTGGHCGFPMAD--KQ-G-LYWSEKRALEFVS---\n+--------\n+>313606.M23134_04462\n+MPV------------------------IS-ESSY-RSPF-WLPNRHLQTI\n+YPNILRRIEGVHYQRERIDTPDGDFLDLDWCKSPSG--------------\n+------------------------Q---PRLVIMSHGLEGDTHRTYMKGM\n+VRAFRQQNWDVLTWNYRGCSGENNRLIKAYHSGATYDLATVVQHALSL-N\n+VYQEVVMVGFSLGGNLTLKYLGEQGAQLSELITKSVIFSAPVDLAACADE\n+ISKPHNFIYAKRFLRTLKQKLKAKIERYPD--A-FAPGIMQQIKTLRDFD\n+NLYTAPVHGFENAQDYYKQCSARYFLDTIAIPTLIVNAQNDSFLAPTCYP\n+KTQVEKLDWIFLEIPRKGGHCGFAPAK--P--NDLYWSEQRALEFVQG--\n+--------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,462 @@\n+>880070.Cycma_2247\n+---MNEVYITAMGAYLPNQPVSNDEIEDFLGRIDGKESRVKPRILKQNGI\n+KTRYYALNKAQETTHSNAELAVNAVNNALKKSNLKASDVELLCTGTSQGD\n+LPIPGFASMVHAGLDFK-RCELASFQSVCASGVMALKNAFAQIKSEQKQN\n+AVCVGSELPSRMFKASRFE--------AQEVKP-LPFDAEFLRWMLSDGA\n+GAFVLQNKINLKGLSLRIDWIDIKSFANEFPVCMYTGKIDNEDEAE-KTW\n+LDYPSYEEASKAGAINLHQDTRLLD-KLIKTGVAHYFELIDQGKVKVSKV\n+DWLCCHYSSEVFKDSIKELMQKGGGAIPDDKWFSNLSAKGNTGSASIFIM\n+VEELMYSGKLKKGDSILCMVPESGRFITSFMHFTVVGKS-EESKIYPQRE\n+--IAPPELIIDTNETSEWLIRNLARVWIDFETALLFETALLKVPIVAKIH\n+DGSLSMADYKLLLTDLRQQVIDGSQWISRAASNIDIDLFELRSAFIKHTA\n+TEHKDYQMLERNFEALGENLETIRSGEKNIGTVALTSFMFQQASKANPVD\n+LLGSMFIIEGIGKRLAGYWGKLMQDQLQLNNSQVSFFTYHGTAD--ENHF\n+HNLEEALNHPKMNLEVAKKIVKTAKITAKLYRMQLEELGNY\n+>700598.Niako_1446\n+MSSLNPVYITAAGAYLPGAPVSNDEVEEYLGYLFGKPSRTKQRMLKQNGI\n+TSRHYAIDKNQQTTHTVSGMTAAAIQNCLQKAGVAKKEIEFLSAATTQGD\n+LPVPGFASMVHADAQLE-QCEIASHQSVCAAGMMAIKNAWLHMRTGEADK\n+AIACAGELPSRMFKAQRFEHQAM-----VKEKNQLDLETDFLRWMLSDGA\n+GALLLENQPARNQFSLQIDWIDLRSHAHLYDVCMYAGKNK-NNG--KDSW\n+IDYNSFSEADNDAAINLKQDLKIVH-NIVHLGVQHFFNLIDEGRINPNQL\n+DWLLCHYSSEYFRPQIVDLMQKGGCNIPPEKWFTNLHTRGNTGAASIFLM\n+LEELLYSGKLKAGQKLLCMVPESGRFITSFMQLTVVAPASAAPALSIHAD\n+DAIEAPVIRTNGMPVQEWLVRQLTSVWVD------FESSLRQVPVVQKIY\n+NGSLSMEDYKLLLVNLRQQVIDGSQWIARAASNITIEYFDIRSAFITHSR\n+DEHRDYQILEKNYLACGGTYEELRQGEKNIGSEALSAFMFHKASQPNPFD\n+LLGGMFIVEGLGNRLAGKWGRAIQEQLQLQDDQVSFFIYHETSDANDNHF\n+ERFEKAIQSDLLQEAIAARIVKTAKITARLYAMQLQELGNY\n+>485918.Cpin_2173\n+--M-HKVFITATGKFLPNTAIPNEAMEDYLGRINGQSSRTKDIFLRKNGI\n+KSRYYALDTQQQTTHQAYEMASKAIDDCLEGAAAGKQNIDFLSTATTQSD\n+LPVPGFASMVQGESGIG-TCTLASHQSVCAASIMAIQNAYMHVQAGQSRN\n+AVSCAAELPSRMFKASRFAGQSI-----VGTDAALPADIDFLRWMLSDGA\n+GAMLLQPVPSRTGVSLEIEWIDLRSYAHQYDLCMYTGTNKQADGSISKTW\n+LDYESMSAADKDGAINLKQDMQLVD-NIVKLGIQRFFELVDEKKIAPEAI\n+DWLVCHYSSHHFKKQITDLLEKGGADIPAEKWFTNLYTVGNIGSASIFVM\n+LDELLHSGKLKHGQQVLCMVPESGRFITGYMMLRVVA-P-AAPGVVTEDI\n+ATIKAPAIRTQQKPVQEWLVRQLTGVWFD------FERSLQQVPIVKRIF\n+NGQLTLEEYKRLLLNLRQQVIDGSQWIARAASNVSMEYFHVRSSFIRHSS\n+DEHRDYQILEKNYINCGGNEQDLYTGEKNIGSEALSAYMFQRASQPDPFD\n+LLGGMFIIEGLGNRVSGKWGRAIQQQLQLNADQVSFFIYHESSDSNDNHF\n+ERFENAIQSDLLTQAIAQKIVKTAKVVARLYRMQLEELDNF\n+>391596.PBAL39_16134\n+--M-NKVYINATGIFLPNEPVENNQMEDYLGLINDVPSRTKDIFLRKNGI\n+KRRYYALDSSQNTTHKAYEMAALAVKDCIDSSTADYNGIDLLCAATTQSD\n+MPIPGFASMVHASSGIG-RCGIASHQSVCAASMMAIQNAFNQIKAGTAKN\n+AVCCAAELPSRMFKSKRFAGQHA----FSDATAKLPLETDFLRWMLSDGA\n+GAMLLQNSANTGNISLEIEWVDMKSYAHAFEVCMYTGANKEPDGFVEKTW\n+LDYDTISEANVDGAINLKQDMQLVD-NIVKLGIQRFFELTDEGKIEPSGI\n+DWLVCHYSSHHFKSQIVDLLKKGGAEIAPEKWFTNLYSVGNIGSASIFVM\n+LDELLKSGKLEDGQNILCMVPESGRFVTGYMMLKVRSND-QQQKRYVEEI\n+DTIKPPEIRIQSKPVQEWLVRQLTGVWFD------FERGLQQVPIVKKIF\n+NGSLTLEEYKRLLVNLRQQVIDGSQWIARAASNVSMSHFPVRSAFIRHSS\n+DEHRDYQILEQNYINCGGNEEEILTGNKNLGSEALSAYMFHRASQPDPFD\n+LLGGMFIIEGLGNRVSGKWGRAIQQQLNLNKDQVSFFIYHESSDSNDNHF\n+ERFEQAIQSDLLTQQMAEKIVKTAKVVAKLYTMQLEEIDNF\n+>203275.BFO_3187\n+---MNEVFITRTSSFLPNEAVENDNMEQILGMVGGHPSRVRSIILRQNGI\n+KKRYYSLDREGKIVYTNAELTAIAVNKLFD-QAISFKDIGLLACGTSLPD\n+QLFPSHAVMTHGLLGNK-PIDLLSPSGVCCAGMHAFKHAYLSVLSGMSQN\n+AVSTGSELVSPVLRADNFEEEYKMLS-LVEEKPIIAFEKDFLRWMLSDGA\n+GAFLFENRCR-GDLSLRIDWLESISYANELEVCMYAGA-IFENER-FKSW\n+KEADP-LEWGRESYFAVKQDTRLLGAHVIEKGVDFVCENLCKHDIGFNEI\n+DYVLPHISSMYFFDKLKKGFEMKGYPVADGQWFLNLPYVGNVGSASIYLM\n+LDELFHSGKLKQGHRVLLIVPESSRFSYSVALLTVV--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n+>714943.Mucpa_6793\n+----MPVYINRTSAFFPNSPVPNDDMELYLGYINGKPSKSKSIVLRNNAI\n+VNRYYALDKGGKSTHTNAQMTALAVKELFKDEPEDIKTIELLSCGTSSPD\n+QMMPSHGVMTHGWLPEAGPIEVVSPAGVCCAGMHALKYAYMAIRTGDVKL\n+AVATGSERFSGLLVSDVFEEEAQKLV-ELNANPYIAFQKDFLRWMLSDGA\n+SAFLMSDEPNKEGISLRLDWIEGVSYANEMETCMYMGGEKQADGT-LKGF\n+MDYTP-EEIMNKSIFSVKQDITLLSDNIVPLGGKKIKEIFERRGLTAADI\n+DHFLPHISSDFFKSKIYDLVEIYGGGIPYEKWFINLYTVGNVGAASVYLM\n+IDELFNSGRLKVGEKILLLVPESSRFSYMYAMLTVV--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------'..b'NF-PMEIFSSAGVCLTSLQALKICYSNILAGLHKK\n+AVCVASELTSPALVSKFYDPEYEATHENPDKDPYMAFEKDFMRFMLSDGA\n+GAVLVQDHPE-GNTPLRIEWIEMTSYANELPTCMFMASELQADGR-LKSW\n+KEFTP-DEIKERGVLVGKQDIRHLKKFAIKYWVNHIETVLAKHNVKPEEI\n+NCVIPHLSSMLFYDKLNDEFLARKIALTKEKWFVNLPSVGNVGSAAIYVA\n+LEELIRTKEIKRGNKILLLVPESGRFSYGTVLLTSE--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n+>767031.HMPREF9137_1626\n+--MEKAAYINSVSAYLPNSPIANEDMEDYIGKIGGNPSRVRSIVLRQNGI\n+KTRYYGLDKNQSLTHSNAELAKEAVCGLFE-NGNIPDDLTLLACGTSTPD\n+QLLPSHASMVHGELANY-PMEIFSSAGVCLTSLQALKICYSNILAGLHQK\n+AVCVASELTSPALVSKFYDPEYEATHDNPDKDPYMAFEKDFMRFMLSDGA\n+GAVLVQDHPE-GICPLKIEWVDMTSYANELPTCMFMASELQEDGR-LKSW\n+KEFSP-NEIKERAVLVGKQDIRQLKKYIIKYWVDHIETVLAKHHVKAEEI\n+DYPLAELKCSY----------------------------NDIQKVAHVVD\n+FQ------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n+>866771.HMPREF9296_2108\n+--MEKAAYINSVSEYLPNSPIANEDMEDYIGKIGGNPSRVRSIVLRQNGI\n+KTRYYGLDKNQNLTHSNAELAKEAVCRLFE-NGSIPDDLTLLACGTSTPD\n+QLLPSHASMVHGELANY-PMEIFSSAGVCLTSLQALKICYSNILAGLHQK\n+AVCVASELTSPALVSKFYDPEYEATHDNPDKDPYMAFEKDFMRFMLSDGA\n+GAVLVQDHPE-GICPLKIEWVDMTSYANELPTCMFMASELQENGR-LKSW\n+KEFSP-DEIKERAVLVGKQDIRQLKKHIIKYWVDHIETVLAKHHVKAEEI\n+DYVIPHVSSMFFYEKLNDEIAARNIALTKEKWFTNLTSVGNIGSAAIYVG\n+LEELIRTKGIKQGDKILLLVPESGRFSYGTVLLSA---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n+>553171.HMPREF0648_0777\n+--MEKAAYINSVSAYLPNSPIANEDMEDYIGKIGGNPSRVRSIVLRQNGI\n+KTRYYGLDKNQSLTHSNAELAKEAVCGLFE-NGSIPDDLTLLACGTSTPD\n+QLLPSHASMVHGELANY-PMEIFSSAGVCLTSLQALKICYSNILAGLHQK\n+AVCVASELTSPALVSKFYDPEYEATHDNPDKDPYMAFEKDFMRFMLSDGA\n+GAVLVQDHPE-GICPLKIEWVDMTSYANELPTCMFMASELQENGR-LKSW\n+KEFSP-DEIKERAVLVGKQDIRQLKKHIIKYWVDHIETVLAKHHVKAEEI\n+DYVIPHVSSMFFYEKLNDEIAARNIALTKEKWFTNLTSVGNIGSAAIYVG\n+LEELIRTKEIKQGDKILLLVPESGRFSYGTVLLTAD--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n+>667015.Bacsa_1059\n+--MENDVFITGTSCYFPNAPVFNEYMEDYLGLITGQHSRVKPIILKQNGI\n+KQRYYALTKEQKITHTNAEMAVYSIVKLLEQSSIVDQDIELLSCATSSPD\n+QMLPSHASMVHGLLKKK-PLEIFSASGICLSCLQAFKVAYWGILSGEKKN\n+AICSTSELTSATLLSKNYDIEYEKCA-DLGVQPYMALEKDFLRFMLSDGA\n+SAVLLQNSPG-TGKALRIEWVEMVSYANELPTCMFMGAEKREDGE-LKSW\n+KVFSN-QERIDRSLFVVKQDVKLLGLKAVPYWAKHIKSCLEMHSVSPDSI\n+SYVIPHVSSMFFYDKIINELKNVGVGIDESKWFTNLPKVGNIASAAIFAA\n+LDEFWRTHELKSGEKILLLVPESGRFSYGTVLLSVV--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n+>483216.BACEGG_00426\n+--MKKDVFITGLASFFPNSPVSNDEMEEFLGLISGKHSKVQRIVLKQNGI\n+KRRYYALNKNQEITHTNAEMAMLAIRKLLALTNKSQKDIELLACATATPD\n+QILPSHASMVHGLWE-E-PVEIFSSAGVCLSCLQALKIAYLSIAASEKQN\n+AICSTSELVSAMLLSKNFDIEYERCC-NLGTNPYMALEKDFLRFMLSDGA\n+SCALLENHPGEKGVSLKIEWIEMDSYANETPTCMFAGAVRREDGE-LKSW\n+KSFES-QELVDESLMVIKQDIKLLGTKLMPLWIRHIKSCLNKHGMTPDDV\n+DYVIPHSSSMVIYGNLIEAMKNESFELYKREWFTNLTWVGNIGSSAILAA\n+LDEFCSTRKLKSGEKILLLVPESGRFSYGTVLLSVV--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,372 @@\n+>679937.Bcop_1516\n+---------------MN-----K--L-STKQFWMVGLMLFSLFFGAGNLI\n+FPPMVGKMSGTSMYSSMLFFSITAVVLPVLGVIAVAKSKG-LINMGKKVS\n+PWFATLFTIIIYLSMGPLMGIPRAGTVPFEIGIAPNLPEGFASRSALFVF\n+TLLFFSTTYWLCLNPMKMAERVGKYLSPILLVMMVLLFICSLINPMGSPI\n+QPQAEYAS-NP---YISGFIEGYMTMDAMGALNFGLVIAMVIHS------\n+-------------FHIKEERAVIHSTIKTGVLAGVLLFGIYMMLAHLGAT\n+SISLYP------QTTNGAQILNAASKHLFGSFGAILVAGIFMLACLTTCI\n+GLTTSSAQYFATWT-K--------KFSYKSWVRIWIICSLLLANVGLDAI\n+LNYSGPILTALYPVAIVMILLVIADSLFNGEQAVYKITVYTTGIVSILNG\n+LSELGIQ-IPLITKAIEKLPLYSLQLSWVIPAIVAFTVGCIYIKAKKTRL\n+ITSVVEDKS\n+>525373.HMPREF0766_10243\n+--------------------MR-----KITDITTLGFALFAMFFGAGNLL\n+LPPLIGLAAGQYWGLAISGFGLTGILLPFLGVLSVVNSGETFEDLAGRVH\n+RTVALVLGAVIMLGIGPLIAIPRTAATTYEVGLLPTFPSLS----PI-WG\n+SVLFFVVTYVLSIRPSKVVDVIGNFLTPVLLVLLLTLIIIGILYPV-SDP\n+GTGTGTPV-AA---FTSGFTEGYQTLDVLASVIFAGIIITAARMKGY---\n+-------------TSLKEKN---QIVISAGLMAAIFLLLIYGGLVILGAT\n+SGYSTG------NDIKRAELLLFISNKILGGYGTIAISLSIALACLTTAI\n+ALTCAVGTFFSTLF-KN-------KISYEVIVTICCLLSGILSITGVEYI\n+IEVAYPFLAFIYPIVITLVLYVIIFGKKISSKLPYIGAVAGTTLVSTVYL\n+LAGLGI-HLAGAERLVHAIPLAEYELWWVLPSFIFFLLFWLIDRFKTKTT\n+KDT-----V\n+>865938.Weevi_2070\n+--------------------MKN--I-NIRTIITLGFALFAMFFGAGNLI\n+LPPFIGLETGDQWLYGIIGFGITGIIGPFLGLLAVIFSGESFFDLGKKIH\n+PLFSVVMGTIIMLCIGPIIAIPRTSSLTYEIGIQPFFPYIN----SY-VG\n+SFVFFAVVIALSFSKSKIVDIIGNFLTPVLLLILFYLLYVGIINPV-STD\n+YESLVSKS-AA---FGFGFVEGYQTLDVLASVIFAGIIIGATQTKGY---\n+-------------HTIKERT---RVSIFAGLLAIFFLLIIYGGLVYLGAS\n+SG-VTN------HSIFRTELLISIAHTLLGSSSTILLSICIALACLTTAI\n+ALTGAVASFFEQIT-RG-------FLPYKIGVLLCSFVAYMFSIMSVDEI\n+IEFAVPILVFVYPIVLTLVLFVVLFSRTIKGKLPYIGAVIGTAMVAALGF\n+LQHFNL-LNEPLIALRESLPLYAYELEWLLPAIGFFVVFCLVEYMLKSRN\n+ISR------\n+>553178.CAPGI0001_0884\n+MLQCYPFVIFLYLCAICITYMNK--K-KFLTLTTTGFALFAMFFGAGNLV\n+IPPYIGLKMGAASGAAFVGFFLSGILIPFLAVLMVSSIGTSFTDLGKRFP\n+APFVNSLVVLIIVVFGPLVCVPRSGSTTYEVAIESFFPMVG----KV-TF\n+GVIFFTITLFLALSRSKLVDIIGRWLTPILFLSLIVLIVEGTINAP-KGL\n+TDNGLNFK-EA---FTFGFSKGYLTLDVLSGVIFSGLIISAIIQKGY---\n+-------------SSERQKR---EITILSGMIAAGCLVFIYGGLLYLGAT\n+SDVVTT------EEVKYIDILKHIAHKGLGNNGAIVISVAVAFACLTTAV\n+AIVSAMGGIFETLS-HG-------RIPYRWGVWGCTLVSFVLSIQSVDQI\n+ILYAGYILDFVYPITIALTLFILLFGKRVQKKTPYIIGVSFTAVFSAIFV\n+IGNLM-E-SQTLKGIQDSLPLAQYHIEWLLPAFAAFGVGAIINNK-----\n+---------\n+>521097.Coch_0950\n+--------------------MDK--K-KFITILTAGFALFAMFFGAGNLV\n+IPPYIGLKIGALSGVAFAGFFVSDILLSFLAVVMVASVGLTFTDLGKRFP\n+PLFVNALVFLIIVTLGPLICVPRTGSTTYEVAVQPFFPQIG----KI-TF\n+GVLYFGITLLLSISKAKIVDIIGKILTPFLILSLTILIVVGTINAP-KEL\n+VDNGYSFG-EA---FAFGFSKGYLTLDVLAGVIFSGLIISSIVQEGY---\n+-------------RSEADKK---QVTILSGVIAAGCLVFIYGGLLYLGAT\n+SNLSSS------EGISYIDILKHIAYNVLGDNGGIVISVAVAFACLTSAI\n+AIVSAMGEIFENIS-KG-------RIPYKWGVWICTLVSFALSIRSVDEI\n+IHYAGYLLDFSYPITIALTLFVLFFGKRVQSNAPYIVGVTLTAILSGLFI\n+IGDLL-H-IAWINNFKALLPLADYRIEWFIPAFLSFIITAIIVKRV----\n+---------\n+>860228.Ccan_01730\n+------------------MNSPK--R-RIINTTTIGFALFAMFFGAGNLI\n+LPPYIGLTSGSQWFAALLGFFVTAILAPFLGLLMVIRTGTSFVDLGKRVH\n+PQVISVIAFLIILCIGPLVAIPRTGATTFEVGISPLFPSLS----NI-IF\n+AFIFFGIVLVLSISKTKIVDIIGKFLTPFLLVSLAVLVLMGIVNQP-TPI\n+STSPLDFS-KA---FVLGFTEGYQTLDVLAAVTFAGIIISAVMSYGY---\n+-------------VSVKERS---QITIAAGVISTLALVFIYGGLIYLGAT\n+TTYETS------QNVSRTDLLLHISKSILGSNGTYVISVAIAFACLTTAI\n+ALTSAMGDFFERVS-RG-------KIPYRWGVIGCTIISLLLSVNSVDQI\n+ISYAVNILLFIYPITLALIVYILIFGKLVKAKFPYLGVLIVTGLISLISV\n+LENLQL-NFGGLFRFKNSIPLSEHSLEWLLPSFITFVVLALVNQFAIKHR\n+---------\n+>873517.HMPREF1977_2185\n+-----------------MHHIRK--S-KWKTITTVGFALFAMFFGAGNLI\n+LPPFIGLRTEGEWGMALLGFFITAILAPFLGVLMVAKTGTHFTDLGKKTH\n+PWLIKILTLLVILCIGPLVAIPRTAATTFEVGIQPLLPAFP----KV-WF\n+IVLFFAVVTALSISKSKIVSIIGRFLTPFLLIVLVLLIVLGVCFPP-DSI\n+TSTAFTAT-ES---FSLGFLEGYQTMDLLASVIFAGIVIAAVIDSGY---\n+-------------TSRNERV---SVTFAAGMLSTLCLLFIYGGLIYLGAT\n+TDYPLT------DSVQRTELLLHISHSVLGKWGTITVALAIGFACLTTAI\n+ALTSAVGLFFEEVT-HQ-------RIPYKVGAIVCTLISLVLSINTVDNI\n+INYAIYILLFIYPIVSTLIITVLFFDRFVNSKLPYILSVLVTAIISTIDS\n+CQMLEL-PFDKLYEIKSLLPLSHYGLEWFLPALLTFIITAFIKGFQKK--\n+---------\n+>521097.Coch_1310\n+-----------------MHHIRK--S-KWKTITTVGFALFAMFFGAGNLI\n+LPPFIGLRTEGEWGMALLGFFITAILAPFLGVLMVAKTG'..b'LITAAIASLIGIFVGSYQVDFI\n+ITLAVPALMFLYPITIMLILLNIVPNKFA-SKLVFRGVILVTFIFSIPDF\n+LGFIIPR--ENLTGIKSIIPLAENSLGWVLPALFTFAILNLSTFKSEKDK\n+LQ------A\n+>886377.Murru_1456\n+---------------MKTNYQQS--T-GKKSLIITSFALFSLFFGAGNLV\n+LPPLLGFKSGDLWWLVTLGFCISGVLIPILGIIAHAKLQGTLFDFAKKVS\n+PTFSVVYCYLIY-AIAIALPSPRTASVTHEMAVQPFSD-SS----SL-LT\n+SLIYFMLVFVFVINRSKVLDTLGKLLTPGILIILLIMIATAVFALD-FDF\n+VPSEM--G-QP---FSSGILEGYQTFDAIGAVVVGAVIIISINLKEK---\n+-----------A-ASFKDKK---RLIGRAGLWAGIGLFLVYGGLILTGAL\n+FGDAFD------TDISRTALLRGISTKTLGQTANILLSILVSLACFTTAV\n+GIVTGTSDFIKGRFNNA-------ISAYRITAFIGCSLGVLVGQFDVGYI\n+ITVAVPSLMFIYPITIILILLNVVPKKWG-SPKVFQRVIGVTILFSIPDF\n+LGSIGLG--GFISPYVDWIPLGQHQMGWVFPALIAFIVSNITNSKETAAS\n+--------S\n+>867900.Celly_1509\n+-------------------MYPM--N-NTKETLVSAFALFSLFFGAGNLI\n+LPPFIGFNSGELWWVMAIGFCLSAILIPILGIFAHAKLQGTIFDFGKKVS\n+NTFSLVFSILIY-CIAVALPSPRTASVTHEIGIAPFFN-IP----SI-YT\n+SVVYFGLVLVFALNRSKILNILGKFLTPAILLILLAIIGICVFSFD-FTF\n+GASTV--K-SP---FTDGILEGYQTFDAIAAVVVGGVLIISINLKNK---\n+-----------D-ISYTDRK---TLIRNAGIFAGLGLLFVYGGLILTGAL\n+MHSNFN------ADINRTDLLNGISRTLLGNEGNKFLSILVSLACFTTAI\n+GIVTGTADFIKGRFNNS-------NKAYTITAIISCVLGIVMGQFNVDYI\n+IVVAIPALMFIYPITIILIVLNVLPDKYT-APKVFKAVVYTTILFSVPDF\n+LNSIGIT--SVAKFTAAYLPLSTYSLAWVLPATIALVIGNLSSEKATTV-\n+---------\n+>688270.Celal_1609\n+----------------------M--Q-NTKETLVTAFALFSLFFGAGNLI\n+FPPLLGFQSGNMWWLVALGFCLSAVLIPLFGILAHAKIQGTIFDFGKKVS\n+RTFSLMYSILIY-AISVSLPSPRTASVTHEIAVQPFFD-SP----YI-VT\n+SIIYFSLVFIFVMNRSKLLNILGKVLTPAIILILLAIIGITVFYFD-FNF\n+GTTHF--D-NP---FTYGILEGYQTFDAIGAVVVGGVIIVSVNISNK---\n+-----------E-KTFEEKR---VLIRKAGWLAGIALFVIYAGLIFTGAV\n+MHNQFD------ADITRTALLNSISIKTLGSTANLFLSILVSLACFTTAV\n+GIVTGTSDFIRHLFNDS-------QIAYIITAVLGCVLGVVMGQFNVAYI\n+VNVALPALMFIYPITIVLILLNILPEKYA-STLVFRSVVIVTAIFSIPDF\n+LSTIGYD--NEVIFLEELIPLSKYNMGWVIPGFLSFAIVNVLGSKKPIHE\n+---------\n+>313603.FB2170_05320\n+----------------------M--I-KTKETLVIAFALFSLFFGAGNLI\n+LPPLLGFKSGDFWWLVTLGFCVSAVLIPILGILAHAKLQGTMFDFGKKVS\n+PTFALVYSFIVY-AISIALPSPRTASVTHEIAIQPFFE-SS----SL-VT\n+SFIYFGLVYLFVINRSKILNVIGKILTPAIISILLLIIGVATFSFD-FDF\n+GEIIF--T-KP---FTDGILEGYQTFDAIGAVVVGGVIIISINLRKK---\n+-----------N-ASYAEKK---SLIRRAGWLAGLGLFLIYAGLIFTGAL\n+MHNEFD------ADISRTALLNGISIKTLGNTANLFLSILVSLACFTTAV\n+GIVTGTADFMKYKFGDS-------QLAYTITAIVGCVLGVVMGQFDVHYI\n+IAVAVPALMFIYPITIILILLNVMPEKYT-SPLVFKAVVVTTILFSIPDF\n+LGSIGFE--NSIASIKELIPLGTFSMGWVLPSLLVMLLVNALRK------\n+---------\n+>50743.SCB49_06957\n+----------------------M--S-FNKQTLIVAFALFSLFFGAGNLI\n+LPPFLGYNAGTSWPLVSIGFAISAVIIPIMAIYGHARLQGTLMDFAKKVS\n+PLFALIYALIIY-AISVTLPSSRTASVTYEMAIVPYFS-MS----SL-TL\n+SALYFALVLVFALNRTHILSLIGKFLTPFIILILLVIISIGLFADV-TPM\n+SDTIF--K-NT---FTDGILEGYQTFDAIAGVVVGGVIVVSLALQGT---\n+-------------LNYEEKK---TMIAKAGLLAGFGLVLIYGGLIALGAT\n+YNTTIV-------TEDRVQLLTDLSQSTLGNIGTSFLGVLVALACLTTAV\n+GIVTGTADFAKKIAGNS-------QVAYVVTAVVSCIIGVVVGQFDVHYI\n+IDIALPALMFIYPITIALIILNVLPQKIA-SPLVFRLVVIVTFLFSIPDF\n+LQFFTTS--ETLDVIKTYIPFAGVSMGWVLPALFAFVVGNLIGFRGRG--\n+---------\n+>313590.MED134_11125\n+----------------------M--R-MTKQTFITAFALFSLFFGAGNLI\n+LPPFLGYNAGSSWWLVLLGFIISAVVIPILAIYGHARLQGTMLDFAKKVS\n+PLFALLYGIIIY-AISIALPAPRTASVTYEMAIRPYFD-IS----SL-TL\n+SSLYFILVLVFVLNRSKMMDIVGKYLTPAILIILAIVIGVGLFGEY-EPM\n+RASIF--D-NT---ITSGILEGYQTFDAIGGVVVGGVIVISLGFKN----\n+-------------STPTENK---RIITQGGIIAGLGLLFIYGGLIYLGAL\n+RSGGAE-------VTDRTALLSMLSVDTLGAVGSRVLAVLVSLACFTTAV\n+GIVTGTSDFVKGIFNNS-------QLAYNITAVLGCVLGVVMGQLDVMSI\n+IAVAVPALMFIYPITIVLIILNALPDKWT-TVLVFRSVVIATILFSAPDF\n+WASLGFS--EQMKGIKEFIPLGTVSLGWLLPAVITLIAVNVFTLSRKRTT\n+---------\n+>983548.Krodi_1507\n+----------------------M--R-MTKQTFITAFALFSLFFGAGNLI\n+LPSFLGYNAGSSWLFVLAGFLISAVVVPILAIYGHARLQGTLIDFAKKVS\n+PLFALLYTIVVY-AISIALPGPRTASVTYEMAIAPYFE-IS----SW-LW\n+STIYFGLVLLFVLNRSKMMDLVGKYLTPAILIILALVIGIGIFGEY-EPM\n+RASIF--D-ST---LTSGILEGYQTFDAIGGVVVGGVIVISLGFKE----\n+-------------GSSRAKQ---RLLTRAGIIAGIGLLLIYGGLIYLGAL\n+RSGGIE-------MTDRTALLNLLSTDTLGVIGTKVLAVLVSLACFTTAV\n+GIVTGTADFVKGILGNS-------QVAYTITAILGAILGVVMGQLDVNSI\n+IIVAVPALMFIYPITIVLILLNAMPRRWT-APVVFRAVVIATILFSAPDF\n+WASVGFG--DQMKVLQEMIPLGTVSLGWLLPAVVTYIMVSAITLSRKRTI\n+---------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,720 @@\n+>309807.SRU_1408\n+---------------------MDA----P---T---DLGRTSALQAAQSP\n+AITRSILVVSALFLVVLGVALAFVPWRQTVSGSGEVTAYAPEARPRTVES\n+RISARVADWHVVEGDEVAKGDTVAVLEDLGSSYLDDQFADRVAAQRTNTL\n+NGL---------------------RLEVERARQKLAQARQKRRSADEKVS\n+NATLGVSTARTRLARIEDLQDD-GISSVRDLETARLKFQKARTDSVAAAA\n+DLAAARRAVESARLNVERKEQKL---------------------EAKQAA\n+LSRKVGNARERASNAIVRAPISGTVSSINRVGPGQIVKKGTTLATVAPKT\n+DDRAAELFVSSIGASLIEPGRQVQLQFSGFPALQFSGLPDASTGTFTGTV\n+RFIDPVGDGSGRFRMLVVPDT---S---DTTSWPSPEYLRQGAPAKGSVL\n+LSSVSLGYEIWRRMNGLPPQLSTQQGTAP--AK-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n+>313606.M23134_00723\n+--------------------MLEIS-NEKIDYK--EINEKVHSLKTLTPP\n+RNARRLAY-ILILLLLILIGILFLPWQQNISATGKVTALRPSDRPQVVQS\n+TIAGRIKEWRIQEGQSVTKGDTLAIISEVKSDYFDPQLLKRLEEQVTAKR\n+EGMEANQGKVRALDQQISALQDAQKFSLEKARNKYEQARLKVISDSANLQ\n+AEQVQYGIAKSQFGRYDSLYRNDGLISKTDWEKRQLKLQNTYAKVVALQN\n+KLLISKNKLINARIEFNSLIADYTGKIFKSQSEKNSTQAYVANSRGELSK\n+LRNKYANIEIRNQQYYVLAPQNGFVVKALKSGVGEMIKSNEAIATVMPAN\n+PSIAVELMVPARDVPLIEKGRHVRLEFDGWPALQVSGWPSVSVGTFGGQV\n+KVIDYIISKGGKYRLLVVPDP--E----Q--DGNWPKQLRAGSGVYGWVM\n+LKDVPIWYEFWRKLNGFPPSLYEEPNDDLQDKGGKKKKK--AK-------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------------N\n+>761193.Runsl_4087\n+--------------------MLNLS-NHRVNVP--SIEKEVNSLNTLHSP\n+KTAKIVYR-WISGIVIGLLLVMFLPWQQNINGKGYVTALTPQDRPQNIQN\n+AVAGQILRWNVREGDYVKKGDTILVITEIKDDYFDPQVLVRTQEQIQAKI\n+DGIAAYKAKIEATDNQISALRQGLQFSLEKARNKLIQAQMKVRSDSADMV\n+AVNRNLQIAKERLDRAEVMYK-EGTISLVDAETRRLKFQEDQAKMVAQTQ\n+KLSISRNELINARIELSSVEADYRKDIAKAFSDRSTALSSVADGESELSK\n+LQNKYENIRIRRDQYVVRSPQDGYVVKSLKAGIGETIKEGESIITLQPRQ\n+PELAVELYVKAMDLSLINPGRHVRLEFDGWPALQFSGWPGTSVGTFGGTV\n+AIIDRVNSKNGQYRLLIRSD---HTG-NE--NEQWPDQLRIGSGVNGFVM\n+LKDVPIWWEIWRQLNGFPPDYLADIYPEEGEKEAKK--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n+>504472.Slin_3996\n+--------------------MLNIS-NQRVDEQ-LFNHYPLKTLHTLPQP\n+DAGRRLGR-WMLIILFISLAVLFLPWQQNINGEGSVTALTPQDRPQTVQN\n+AIAGRIERWKIQEGQSVRKGDTLLVISEIKDDYFDPNLPLRLDEQLDAKR\n+GSLTATGAKIAALDEQLSALQTGLQVKLASARNKVRQSQFKVISDSTDLI\n+AVQKNYQIALDRLDRFEKGYR-NGLFSLTDLETRRLKVQEDNAKVIAQEN\n+KLNVSRQELINSRLDLNTIQADYQEKIAKTMSDRSSAVSYRAEAEGEISK\n+IQNKISSVDVRRGLYVVRAPQDGFVVRSLKAGIGEMIKEGESIATLQPAH\n+PLVAIELYVRPMDVPLIQRGRTVRLQFDGWPAIQFSGWPSVAVGTFGGEV\n+AVIDAVNSVNGKYRLLVKPK----VQ-KG--DQPWPQQLRVGSGVYGWVM\n+LDNVPIWYELWRQLNGFPPSLKEEPKEES--KK-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----'..b'----------MLNIS-QDKINEK--VDISGYKASKKVLEK\n+KHYAYFNR-FLKVFSIILIIVLFLPWTQTISGIGYVTTLTPEQRPQTIQS\n+PIPGRIEKWYVREGDFVEKGDTILFITEVKNEYFDPNLVERTDQQVRAKA\n+SSVESYRNKVNALGNQIEALRNERVLKLQQAENKRIQAELKIKSDSIDFE\n+ATKTNLRIAERQYERTLGLQQ-EGLKAVTDVEEKRLKLQEAQAKIISQEN\n+KLLASRNELLNAQIELNRLEATYADKISKAQSDQATALSTQLDTEAAVSK\n+LENTRTNYEIRNALYYVRAPQSGYINKAIIGGIGETFKEGQQLVSIMPSD\n+FDIAVETYVKPIDLPLIHNGEKVRIQFDGWPSIVFSGWPYNSFGTFGGKV\n+VAIERFISPNGKYRVLLAPD---P----D--EQPWPEALRIGAGASTLAL\n+LEDVPIWYELWRKLNGFPPNYYTPSDSND--SKEKDK-------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------------K\n+>391603.FBALC1_13572\n+--------------------MLNIS-NNQLNKS--IDITKSKSGKRVFYG\n+RYYKYFNR-FLGAFAIVGIIIMFLPWTQNITGGGQVTTLTPDQRPQNIQS\n+PIPGRIEQWFVREGDFVAKGDTIMKISEVKSEYFDPNLVQRTTQQREAKA\n+LSVTSYGEKVKALNRQIGALSQERGLKLEQARNKLIQSKLKVQSDSIDLE\n+AAKTNKQIAQRQFDRTVTLQE-EGFKATKDVEDKRLKLQGTEAKLISQEN\n+KLLASRNEVINSQVEISRVNAAYSDKISKAQSDMFTAQSSQFDTEAQVTK\n+LDNQVSNYQMRSDLQFVTAPYDGYINKVIRGGVGQTFKEGESLVGIMPAQ\n+VDLAVETFVEPIDLPLLHIGERVRVQFDGWPAIVFSGWPNVSYGTYGAKV\n+VAIENFISDNGKFRVLLAPD---E----E--DHKWPKDIRAGSGAFTMAL\n+LDDVPIWFELWRQLNGFPPNYYQPERAAK--TKTKKA-------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------------------H\n+>688270.Celal_1044\n+--------------------MLNIS-NNVLNEK--VDLSGYKSTQRVFHK\n+RHYKYFNR-FLIGSALFGFIVLFLPWTQNVRGKGSLTSLKPDQRPQTIQS\n+PIPGRIEKWYVQEGDFVNKGDTILFISEIKNEYFDPKLVERTGDQIKAKE\n+RSVVSYEGKVKALNNQIGALATERGLKLQQAKNKLLQAKLKVQSDSIDLM\n+AAATNLEISERQYDRTVLLQE-EGLKAVTDVEEKRLKLQETQAKLISQQN\n+KLLASRNEILNASVAISSVQTAYTDKISKAQSDMYSAQSGQYDSQAQVTK\n+LENQFTNYEMRNDMYYIKAPQSGYINKAIQAGIGETFKEGDKLVGIMPSV\n+YDKAVEMFVAPLDLPLIHKGEKVRIEFDGWPAIVFSGWPNASYGTYGGVV\n+VAVETFISPNGKYRILLAQD---S----E--DQAWPNEIRVGSGANTIAL\n+LEDVPIWYELWRQLNGFPPNYYQPNATAT--KDKK---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n+>886377.Murru_1018\n+--------------------MLNISSNNKLNEK--VDLTGYKAGKKVFHK\n+RHYKQFNR-FLASFSIIVLLMMFLPWTQNISGRGYLTTLTPDQRPQTIQS\n+PIPGRIEKWYVREGDYVEKGDTILFISEIKSEYFDPDLVERTGQQIKAKT\n+MSVSSYQEKVKALNQQIRALNQELGLKLEQTRNKLMQSKLKVESDSIDLE\n+AAKTNILIAQRQYDRTEKLQE-EGLKAVTDVEEKRLKLQETQAKLISQEN\n+KLLASKNNVINAQVEINRVRAEYSDKISKAQSDLYTAQSNQFDSEAQVTK\n+LENQYTNYEMRNKMLYIKAPQNGYITKAIQSGIGETFKEGAQLVGIMPSD\n+YDIAVETFVDPIDLPLIHVDEKVRIQFDGWPAIVFSGWPNVSYGTFGGKV\n+VAIENFISPNGKYRVLLAPD---E----E--EAPWPKDIRVGSGASTMAL\n+LEDVPIWYELWRQLNGFPPNYYQPQNTST--DAKKK--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,790 @@\n+>755732.Fluta_2365\n+--------------------------------------------------\n+--MNILNFLNSFFRIKNAKQRLKGMN-RNF-V--LTVL--LVL--L-TST\n+-------I--FAQP-EKNKNYK-NF----DRRWIHFGFMLGANMANFKAI\n+PVND------A-------YASYN------LKSLETKRQPGGQVGIVGTLK\n+LGHPTIRLR-FVPT-LSFQERAVRYY-FTN--PDPSKT------------\n+----------TDLF-VEERVNSTNLDFPLMLQFRTLRINNFAAYVLVGGQ\n+YSYDLQSQEDANQSL----IDPFVKIRAHDFQGQVGGGLEWFAQFFKFGF\n+EVKFSQSFSSSFIQ--DK--T--------PV---SLPIDRLYNKVLWFSL\n+IFEG\n+>926562.Oweho_1508\n+M-----H---IGNRLVIV--------------------------------\n+-KK------------------------L-R-T-Y-IVM---GLCLVA--M\n+SS-F-------A--QNLPPNQP-KY----DKKPVHFGFLLGVNYYDFHIQ\n+TIE-------------DLSTVPG------YYSVRSETAPGYTIGIIANLR\n+LT-DYLDLR-FIPA-FAATERTLIFD-V---------------------I\n+-EPISE----KRT-EVTRDIQSSFIDFPFELKWKSQRINNYRLYVLGGAK\n+YSYDVSSNEHVED-------DRVFKIPHNDFSYEFGFGVDIYFEFFKFSP\n+QIKGSWGFADLIVD--D---G----------TFYIKGINRLETRGIFLNF\n+TFE-\n+>313594.PI23P_05722\n+--------------------------------------------------\n+--M------------------------KSK-R-V-LFF--FLF--FS---\n+LS-FFAQ------R-ERIAYLP-TF----DDKLLHFGFYLGLNQNDFKLN\n+LKD-----------------GSV------PTDITVAPTTGFNVGLVVDLR\n+LH-KNLNLR-LEPG-LVSNSKRIFF-NH---------------------L\n+---------GTPRD-RIREVASTYLHIPLLFKFSTDRYKNIRPYLLGGVS\n+YDYNFSSNERG-KDN----HSGQFRTKTHNMMYEVGIGIDFYLYYFKFSP\n+SIRGVFAINNEIKY--D--DP----A--NGPSTWTDPINFLGTRGVFLNF\n+AFE-\n+>313598.MED152_11134\n+-----------------M--------------------------------\n+--A------------------------KKV-F-L-LTI--CLF--IS---\n+AS-IFAQ------R-DRVENLP-TF----DKRKLHYGFYLGVNQNDFKLN\n+LRN----------------SNIS------NANITVEPSLGFNVGLIADLR\n+LH-KNLNLR-FEPG-LVTNSKNIYF-NH---------------------I\n+---------DTAQD-SVREIGSTYLHVPVILKFSTDRYKNIRPYVLAGVS\n+YDYNFSSNAENQDDN----SAGQFRMQSHNFMYEVGMGIDIYLNFFKFSP\n+SIRGVFAFNNEIKY--D--DN----P--N--SQWTAPVNFMGTRGIFLNF\n+AFE-\n+>487796.Flav2ADRAFT_1414\n+------------M-R-KK--------------------------------\n+--R----------------------N-KYY-F-L-LLLI-CFS--YS---\n+VG-VFAQYPT-V-R-ERVINLP-TF----DQKPIHYGYFLGLNQYDFKFE\n+YVE-------------NYYKELG------YKDVTVIPKSGFTVGLIGDLR\n+IN-TYFNLR-FEPG-LYYSRRELQY-PD---------------------I\n+-SGF-----EKESD-KIREIKSTYIHLPLILKISTKRINNFRPFIMAGFS\n+TDFNLSSNSKNRDDN----ASNVFRTTAQNLNYELGLGFDFYLYYFKFSP\n+SLRGIFSFQNELVP--D--TD----P--N--SPWTGIINSIFSRGIAIII\n+TFE-\n+>553178.CAPGI0001_0954\n+--------------------------------------------------\n+--M------------------------KKI-T-L-LI-----F--LL---\n+PL-----LAK---A-QPIINLE-DF----DYQKFQWGYYFGINTLDFRVD\n+YQA-------------LDYTNPP------LTDIQTKRSYGFNVGLTGDLR\n+LI-DHLSLR-FEPG-LIYNKRELEF-PF---------------------L\n+-T--------QQTD-RKREVLSTYIYIPVLLKYGSKRWDNFKPYITAGTS\n+VGINLSANNKSRSDN----SEGKFRTQPIVYFYELGFGIDFYTPHFRFTP\n+SIRGLFSIDNELIH--D--SD----P--A--SPWTGNLKGIFTRGVMINL\n+TFE-\n+>888059.HMPREF9071_2274\n+--------------------------------------------------\n+--M------------------------KKI-I-G-IL-----F--VI---\n+PF-----FAK---A-QPITNLE-DF----DYQKFQWGYYFGLNSLDFRLD\n+YQK-------------LDYTTNN------LIDIQTKKSAGFNVGLTGDLR\n+LV-DHLSLR-FEPG-LIYNKRHLEF-PN---------------------F\n+-T--------NDNE-RIRDINSTYIYVPVLLKYGAKRWYNFKPYITAGAS\n+MTLNLSANNRSHADN----SEGKFRVNPTIFFYELGFGIDFYTPHFRFTP\n+SIRGLFSINNELIW--D--ND----P--A--SPWTSNIKGLYTRGIMINL\n+TFE-\n+>860228.Ccan_09030\n+--------------MKIH--------------------------------\n+--T------------------------FFI-T-L-LC-----L--GW---\n+AG-ASSLWGQ-R-K-EPLYNLE-HF----DEKNVQWGYYFGINRFDFKFD\n+YKD-------------LNYSSNF------NKEIDIEKNWGFNVGLSGDLR\n+LI-KYVNLR-FEPG-LVYNQKDLTF-PG---------------------I\n+-E--------GKRN-FLRQVKSTYIYIPLLLKFSSERWYNFKPYATIGAS\n+ATINLSSNQGLSVDN----SERRFRVKKHILFYELGLGLDIYTPYFRMSP\n+SIRGLFSLQNELIP--D--RD----P--N--SNWTGNLNSIKSRGFLINL\n+TFE-\n+>706436.HMPREF9074_01146\n+--------------MNNK--------------------------------\n+--L------------------------KRT-L-L-LL-----F--VF---\n+IG-GFHLYAQ-F-K-QPMINLE-HF----DEKRFQWGYYFGANTFDFKID\n+YKE-------------LNYNNPQ------LQEIQNERKIGFNVGLTGQAR\n+LI-KYIDLR-IEPG-LVYNKRVLTF-PN---------------------F\n+-T--------ENRD-AVREVPSTYIYIPLLLKFSADRWYNVKPYVTAGAS\n+MVFNLSSNANLTIDN----SDRTFRSTKNVFFYEFGFGFDFYTHYFRVSP\n+SVRALFSINNELVP--D--YD----P--N--SRWTG'..b'TLSAKSAHSKMIALTF\n+YFE-\n+>880070.Cycma_1821\n+-----MQNAHIWH-KL-N--------------------------------\n+--I----------------------RWY-KVI-LFSLV--LL--------\n+FF-QNNLVKA-QQK-SFIFNPS-GS----DNEPLSYGFFLAAHNSSLRIK\n+YADNF-LN------P-DYPNLDK------VRAIMPSFSPGFALGFLVTAR\n+LH-DQFNLM-FTPK-VGFYEYRTEL-QLFT--DDPD-AINGVGI------\n+-N-----------A-VPLLTEETLVEIPLLLKYKSQRFNNTRMFFIGGLN\n+GQFRTKNQEEAN--------EDPVALKGSDVALEMGMGFDLYFKFFKFSP\n+EIRFSHGLMNLYQE---------GYS--D--ERMTGAISSIKRKSITIYL\n+NFQ-\n+>388413.ALPR1_04015\n+-----M--------------------------------------------\n+-------------------------------------T--LP--------\n+SF-------G-QGM-FGLTSGS-GS----DNRTISYGFFLAAHTNRYQIK\n+YSDAF-MN------P-ATTSSAG------VQGIYAQNNPGFSLGFIGILR\n+FH-DQVQLL-FTPK-VGFYEYKTEV-RYFG--SEDPSLINTDGYTD---G\n+-N--------INTS-QVLTSEATMVELPLLFKYRSQRFNNTRMYFIGGAS\n+YNFRTKAQDEAD--------IEDLVTTGQDVSLEMGMGFEIYFKYFKFAP\n+EIRFSHGLTNAYRR---------ENT--I--PEIADAISSIKRRSITLYL\n+NFQ-\n+>649349.Lbys_2722\n+--------------------------------------------------\n+-----------------------------------MCL--CLL--SL---\n+GW-ASAQ--------VKTKHQP-NY----DAKPLRFGYYIGFGSTHYITK\n+YRSSF-IQ------Q-ADGTSQA------IYAINSPNTTAIRAGAMINYY\n+IN-DYFDLR-FSPLNITIQKREINY-IKGD--NDQ---------------\n+------------YQ-KDEQVDKAWLEVPVHLKYKSERRLNTRMYVFGGTR\n+WAFETNTVGRKGSKR----SVFNSSLRTNDLMLEYGAGLEIFRPYFKVTP\n+ELHFSHGLFNMIRK---------NN---S--VAYLQDVKSLRTHTVSLII\n+LFQ-\n+>761193.Runsl_1724\n+-----MHTTHVWN-LF-D--------------------------------\n+--L----------------------R---W-K-KIIIG--LLI--SS---\n+GL-VHASIAQ-SVG-YFRKYQE-YY----DDKPIHYGFLFALPVTRFHLV\n+HDNSF-V------------TQDT------TNRITAPVTIGFRFGFVMNGY\n+LN-DHWDIR-TTPS-VSLYNRAVEY-EYGN--GK----------------\n+-------------K-RRELREATWIEIPLLFKYKSQRRGNSRMYMLAGAT\n+FGFETNVRKRQIPG------SDRLNAKSADLTVDYGFGFEQFLAYTKFSP\n+ELRFSHGIVNLYRT---------ND------PNSTGSIRRLTSHTVTLYL\n+MFE-\n+>471854.Dfer_4024\n+--------------------------------------------------\n+-----------------------------------------MA--AQ---\n+EA-HSQG-----IG-YRRKHLE-YY----DDKPIHYGILFAVPFTRFNIK\n+HSNDF-V------------TKDT------AFVIESPRNAAFRMGFTINAY\n+LN-EHFDLR-TTPS-VSLYERHVKF-RYPN--GT----------------\n+-------------D-RTEKRESTWIEIPLLLKYKSVRRVNSRMYMVAGVT\n+LGLETNVKRNRGGG------VGALDTKSSDFSIDYGIGYEQFFEFFKFAP\n+ELRFSHGLTNMLVP---------GK------NSVGNGISRMRTHTVTLYL\n+NFE-\n+>504472.Slin_6454\n+---------------M----------------------------------\n+--Q----------------------T---G-F-VLLLLG-FVP--GS---\n+TQ-AQTS-----YK-YIRKHLE-RY----DDKTIHYGFFFAAPITRFSVT\n+HSPQF-L------------TADS------AYRIYSPNKPAFRVGFVVNAY\n+LN-DRFDLR-LTPS-VSLFSREVQY-DYPG--GT----------------\n+-------------S-KTEIRESTWIDFPLLLKYKSERRNNSRMYLLAGGT\n+FSVESNVRRKETQG------ASRLSTGTMDFAVEYGLGFEQFFEYFKFAP\n+EIRFSHGLVNLYRP---------GT------NAASIGINKLTTHSVTLYL\n+NFE-\n+>313606.M23134_00474\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------MKFLNYGFFIGAGSTKYIGE\n+HSNAL-GT------S-ADTSSNT------SLLVTPKNSIGLSLGFVMNFN\n+LN-RTWGIR-LLPT-YSIYERNIDY-LFAD--SS----------------\n+-------------S-TTAVVATNMVEVPLLLKYRSQLRGTKGMYLVAGVK\n+PAFSVSAQKAED--------KEILRVANTNISIEYGFGFDVYFSFFRFSP\n+EIRFSHGLGNILIQ---------DN------NRLSTPLQRLSTHNVTLYL\n+HFE-\n+>643867.Ftrac_2975\n+-----MQTANFRN-KL-N--------------------------------\n+--L----------------------HGDKV-I-LFVLG--LLF--S----\n+FQ-A-SA-----QY-YEKENLP-NY----DEQLIHYGFYLGGHTANMKVR\n+YNEAF-LT----------NEFDS------LHSIIPQSTPGFTVGFIFNLR\n+IA-QYLDFR-TMPG-VGLYQYTLNY-NTYD--QAEE--------------\n+------------IT-YQGKKEAFYAELPLLLKYKSQRRKNFRAYMVGGVK\n+PSFEVSGKRPSEIN------EDVLLINTFNLALEVGFGIDIYYELFKFSP\n+EIRFSRGVTNALFD---------RQ------NSYSSPINELVTNSVSIYF\n+QFQ-\n+>269798.CHU_2709\n+--------------------------------------------------\n+--M----------------------K---S-V-SLFIL--SLC--IV---\n+LK-VQAQ------D-PRWTNLP-FY----DDKALHYGFTLGINGSGFQNK\n+VSKSY-F------------S-DT------VTSVSPVYTPGFSLGFIVNMR\n+LH-DHFDLR-LLPT-VGFYSRSIQY-DFIK--T-----------------\n+-------------S-EIQTIESTFVEFPLLLKYKSQRRNNSRLYVTGGFK\n+ASIEAGAKKKQRK-------STDLRTNGFDLCLDMGVGMDIYCPLFKFSP\n+EIRYSHGLLNLLNN---------DP------NVYSSSLSRLSSNTISLFF\n+NFE-\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,256 @@\n+>865938.Weevi_1634\n+------------------MIW----------------------VLVLFIF\n+HWYASLFFQTFFHHRYAAHAMFQMSPFMEKVFHVLSFIFQGSSYLSPYAY\n+GVMHRMHHAYADTEKDPHSPLFDKDIFNMM-WRTRLVYNEIDRNEVEVQQ\n+KFKKG--VPAWRSFDKIAENNWVRASWAIIYILI-------YLAI-----\n+-DAPL-----WT-FFVFIPLHILMSPV---HGV-VVNWFSHKYGYRNFEV\n+NDTSTNFLAKDFLMWGECLHNNHHKFGGRPNFA--VKKGEIDPMFPIIKL\n+MAKANII-QFKPGRLDTEYM-----------------------\n+>700598.Niako_1252\n+-------------------MW----------------------VLIIFIA\n+IWYSSLFCQTFFQHRYAAHQAFTMNKFWERTFYIFTYLTQGSSYLSPRAY\n+AIMHRMHHAYTDTEKDPHSPEYSRNMLQMM-ARTRQIYSSIYKGEYEVEE\n+QFTRNL--PDWPAFDKWAHSTFSRICWILGYTVI-------FLWL-----\n+--SQS-----LW-CLLLLPFVIVMGPL---HGA-IINWFAHKYGYTNFKL\n+KNTSQNLFSVDFLMLGESYHNNHHKSPSAINFG--KRWHEVDPVYPVIRF\n+LASLRII-TLRNDKHKTKNSR----------------------\n+>743722.Sph21_4485\n+-------------------MV----------------------IFIFFIG\n+LWYLSLFSQTFFQHRYAAHGSFTMSKFWERFFFIFAYLTQGSSYMSARAY\n+AIMHRMHHAYTDTEKDPHSPRFSSNIFSMM-WRTRNIYGNIVNNKEPIEI\n+RFLKNL--PEWKGFDRWAHSGVSRLLWVAAYFAF-------FLFF-----\n+--ANT-----YW-WFLLLPIVITMGAF---HGA-IVNWFAHKYGYINFRL\n+RNTAKNLLVIDVLMLGESYHNNHHKHPSSVNFG--NRWHEIDPVYPIIVL\n+LKWLRII-RFPKLTPVI--------------------------\n+>485918.Cpin_4336\n+-------------------MV----------------------IAIFFIS\n+IWYLSLFSQTFFQHRYAAHGAFTMNKAWERFFFIVTYITQGSSYMSPKAY\n+GIMHRLHHAHTDTPLDPHSPSNSSDIFSMM-WNTRKVYQDILHDRTVVEE\n+RYLKNL--PSWDGFDRFANGGFSRLLWVVLYILF-------FVAF-----\n+--ATS-----PW-QYLLLPIVVSMGAF---HGA-IVNWFAHKYGYINFKL\n+KNTSMNLLFVDVLMLGESYHNNHHKHPSSVNFG--RRWYEIDPVYYVIRT\n+LSYFKII-RLVNTSKISPAVAH---------------------\n+>485918.Cpin_4048\n+------------------MTA----------------------ILIFFFS\n+HWFLSLFFHTFFLHRYASHQMYTTSKGWERVFYFCTWFFQGTSFLVPRAY\n+GSMHRMHHEFSDTEHDPHSPHFFKDVWSMM-WQTRKLYNDIYHKKVVLDE\n+KFTKNPPLPVWDALDRFGDFTATRLAWAGIYIAF-------YVAF-----\n+--APA-----WY-WYLLLPIHFLIGPV---QGA-VVNWCGHKYGYQNFEN\n+GDKSRNTSPWGILLLGELFQNNHHKFGESPNF-A-KKWFEFDPTYPVMKF\n+FNFIGII-KLKKAEVKVVNMKAAA-------------------\n+>313606.M23134_06219\n+MQQLSKNYLKLQVKKNFIGMI----------------------IFIFLAT\n+HWYLSLFSQTFFLHRYAAHKMFTMSNFWEKYFYIFAYITQGSSYMSPYAY\n+GAMHRLHHAYADTENDPHSPAYDANPFAMM-WRSKNVYMDIYQKRVDLED\n+RFVKD--LPKWHWFDSWGNNWISRVLWGLSYIAF-------YVVF-----\n+--AEY-----WW-MYLFLPIHFIMGPF---HGV-IINWIAHKHGYRNFEV\n+QDTAHNIMPLDVFMMGEGYHNNHHANGSRANF-G-VKWHEIDPTFVVIKV\n+LNALHIV-RLVPEKVTKAQEKPKETVAS---------------\n+>983548.Krodi_2702\n+-------------------ML----------------------IIFFIVI\n+LWYSGLFFQSFFLHRYAAHQTFTMSKTTEKITFILTWLFQGPSYLSAYGY\n+GIMHRMHHAYTDTEKDPHSPSYDANLFAMM-WKTKTIYQDINNDRIEVDP\n+KFKKN--VPQWKSFDTFASSRLSRLLWVGLYIAF-------FAVF-----\n+--ATA-----WW-QWLLLPVAFAMAPI---HGV-IINWFGHILGYTNFKT\n+KDTSKNLFRFDFLMMGEAYHNNHHKFAARPNFGG-IHWYEIDVTYVIMKV\n+LHRTGVI-KMKPITIDVHSHH----------------------\n+>313590.MED134_05839\n+-------------------ML----------------------ILLFVIV\n+MWYSGLFFQSFFLHRYAAHQTFTMSKTAEKITFVLTWIFQGPSYLSAYGY\n+GIMHRMHHAYTDTDKDPHSPSYDENPFAMM-WKTKNIYQDINNDRVEVDA\n+KFKKN--VPQWKRFDAFASSRFSRVLWGALYITF-------FAVF-----\n+--ATA-----WW-QWLFLPVVLAMAPI---HGV-IINWFGHILGYRNFKT\n+KDTSKNLFRFDFLMMGEGYHNNHHKFGSRPNFGG-VRWYEIDVTYLIMRF\n+LHRINLI-QMKPIKIDVQRHR----------------------\n+>313595.P700755_18927\n+--------------------------------------------------\n+-----------------------MSKTMERITFVLTWIFQGPSYLSAYGY\n+GIMHRMHHAYTDTEKDPHSPSHDANLFAMM-WKTKTIYQDINQQRIKVDQ\n+KFTKN--VPQWKEFDLFASSRISRILWVSAYILF-------FSFF-----\n+--ATT-----WW-EWLLLPVTLAMAPI---HGV-IINWFGHIFGYVNYKV\n+KNTSKNLFPFDFLMMGEGYHNNHHKHSSSPNFG--VKWHEIDMTYLIIRV\n+LDTLGFI-KLKPIPVRS---S----------------------\n+>313594.PI23P_09755\n+-------------------MI----------------------IVIFILV\n+LWYGGLFFQSFFLHRYAAHQVFTMSKTMERISFILTWFFQGSSYLSAYGY\n+GIMHRMHHAYTDTEKDPHSPSHDPNLFAMM-WKTKTIYQDINDQNIVVDE\n+KFTKN--VPQWKSFDAFASSRFSRLLWISFYILF-------FAYF-----\n+--TTA-----LW-QWALLPVALLMAPI---HGV-IINWFGHIYGYVNYKM\n+TNTSKNLFPFDFLMMGEGYHNNHHKHASSANFG--IKWHEVDVTYVIMKV\n+LHFLGCI-QLKSIPAKR--------------------------\n+>688270.Celal_3922\n+-------------------MA----------------------VIIFVLV\n+LWYGGLFFQSFFLHRYAAHQVFTMSKTMERITFILTWIFQGSSYLSAYGY\n+GVMHRMHHAYTDTDKDPHSPSHDANLFAMM-WRTKNIYQDINKERIAIDQ\n+RFTKN--VPQWKAFDKFASSRISRVLWI'..b'PHHTENLFTMM-WKTKNIYNEYFSFRLTPEE\n+RFSKD--IPDWNRFDKFADTMYIRVAWGLLYVLI-------YVLCISVFE\n+LPGTH-----WW-MYFLLPIHFLMGPV---HGA-IVNWSGHKYGYANFDN\n+NDKSKNSLLLDVLMLGELFQNNHHKLPNRPNF-A-VKWYEFDPTYPIVKL\n+LHATKII-KLRTT------------------------------\n+>880070.Cycma_5088\n+-------------------MI----------------------LIIFFLL\n+HWYFSLFCQSFFLHRYAAHQMFVMNKYWEKFFYIFTWFCQGSSYLSPRAY\n+AILHRMHHAYSDTPLDPHSPHHTENLFTMM-WKTKKIYNEHFTFRAKPEE\n+RFIKD--VPDWNRFDKFADTMGIRIGWVLVYVLI-------YVLSISVFE\n+LAGTH-----WW-MYFLLPIHFMMGPV---HGA-IVNWSGHKYGYANFDN\n+NDKSKNSLILDFLMLGELFQNNHHKLPKRVNF-A-VKWYEFDPTYPIVKL\n+LHATGII-KLKPTN-----------------------------\n+>269798.CHU_1595\n+--------------MTGTAWP----------------------IIIFFVA\n+HWYLSLFSQTFFLHRYSAHAMFKMNKFWEKFFFIFLYLTQGSSYLVPRAY\n+GALHRMHHAYSDTEKDPHSPLYSRNAFVMM-WKTKDIYNAVLRREAQVED\n+KFNKN--LPEWAFIDNIGDMWISRIIWGTLYVLF-------YIYF-----\n+VPADM-----WY-LYLLLPIHFLMGPV---HGA-IVNWFGHKLGYQNFDN\n+KDASRNTLALDVLLGGELFQNNHHMYGSRPNF-A-MKWFEFDPTYPVIKV\n+LHYVRII-RLVNPDAKA--------------------------\n+>504472.Slin_1354\n+-------------------MI----------------------VLAAFIG\n+HWYLSLFCQTFFLHRYSAHKMFSMSKFWERFFYALTYVSQGSSYLSPRAY\n+AVLHRMHHAFSDTEKDPHSPHHTKNIFTMM-WKTKDIYNAVLHRKQPVER\n+QFDRN--YPEWSFIEKVGDSWVSRAGWAVMYSVF-------YIFAFI---\n+YLDMH-----WA-FFFLLPVHFVMGPV---HGA-IINWSGHKYGYSNFDN\n+QDQSKNSLILDVVMMGELFQNNHHKRPNAANF-G-AKWFEFDPTFPVIGL\n+LHKLHIV-RLRPSAEAKKAQYEVGHDRRVEEVQKEV---EA--\n+>761193.Runsl_4144\n+------------------MYA----------------------VLAAFFG\n+HWYLSLFCQTFFLHRYSAHKMFTMNKFWEKFFYALTYVSQGSSYLSPRAY\n+AILHRMHHAFSDTDKDPHSPHHTENVFTMM-WKTKDIYNAVLSRKMKVEA\n+RFERD--YPYWEKLEKLGDSWISRLGWGILYSAF-------YFFAFM---\n+YLDMH-----WA-FFLLLPIHYLMGPV---HGA-IVNWSGHKYGYQNFDN\n+KDKSKNSLIFDILMMGELFQNNHHKLPNRVNF-G-TKWFEFDPTYPVIKF\n+LSWTRII-TMKESKVGVEVPSSKAEMMQ---------------\n+>471854.Dfer_0451\n+------------------MYI----------------------VLIVFVV\n+HWYLSLFCQTFFLHRYSAHKMFIMSKPWERFFYLLTYVSQGSSYLSPRAY\n+AILHRMHHAFSDTDKDPHSPHHTKNVFTMM-WETKNIYNAVLNRKRAIEN\n+RFERN--YPEWRLIEKLGDSWISRAGWGILYIVF-------YVLAYI---\n+YLDMH-----WA-FFFLLPIHFLMGPI---HGA-IVNWSGHKYGYQNFDN\n+DDKSKNSLIFDFLMMGELFQNNHHKRPNSINF-G-SRWFEIDPTYPVIKV\n+LNKLKII-EIRKKH-----------------------------\n+>714943.Mucpa_3868\n+------------------M-Y----------------------ILIFFLA\n+HWFLSLFFQTFFLHRYASHKMFTTSRVFERIIYLLDYICLGSSFLNPRAY\n+ALMHREHHAYSDTEKDPHSPHFFTDVFQLM-WATVLTYGDHLKRLKEPES\n+RFTGN--IPEWPLIDRIGSSIASRIVFGLLYTWY-------YVAF-----\n+--ATE-----WW-MYLLLPIHFLMGPI---HGA-IVNWCGHKYGYANFDN\n+NDKSKNSTPFDFLMLGELFQNNHHKHPNSANF-A-KRWFEIDPVYPIMKV\n+MHWVRLI-KLRKAV-----------------------------\n+>485917.Phep_3484\n+------------------M-I----------------------ILLFFLL\n+HWFLSLFSQTFFLHRYASHKMFKMNTFWEKFFYIITFLSQGSSFLNPRAY\n+AILHRMHHAFSDTEKDPHSPHFVKDVWGMM-IQTKNIYLNYSKYNVEPEE\n+QFRDK--YPSWPLIDKIGDSWITRIIFISFYIWF-------YVVF-----\n+--ATS-----WW-MFLLLPIHFLMGPI---HGA-IVNWCGHKYGYSNHDN\n+DDHSKNSLPFDFLMLGELFQNNHHKKPNSPNF-A-SRWFEFDPTYPVMKL\n+MHWMRII-KIRKTDH----------------------------\n+>391596.PBAL39_23567\n+--------------------------------------------------\n+--------------------MFKMNFFWERFFYLITFLSQGSSFLNPRAY\n+AILHRMHHAFSDTEKDPHSPHFVKDVWGMM-IQTKNIYLNYAKYNVEPEE\n+QFRDN--YPSWPIIDKIGDSWITRIVFISFYVWF-------YVTF-----\n+--ATA-----WW-MFFLLPIHFLMGPL---HGA-IVNWCGHKYGYSNHDN\n+NDHSRNSLPLDFLMLGELFQNNHHKKPNSPNF-A-SRWFEFDPTYPIMKV\n+LHWMRII-KIRKV------------------------------\n+>643867.Ftrac_2304\n+MAV--AVKENLKIRKKGTWKKEISFAIVHLLPLGAIWTGATWFDWTVCAF\n+LYVWRMFWVTGGYHRYFAHRSYNTSRWFQ---FLIAFFAQTSAQKGALWW\n+ASHHRHHHRNSDTLKDPHSMLHFGFWYSHVGWII---GSDFKKTDFKVIS\n+DYSKY---PELRWLNK--------NYLVPPVILALTVMALGGLVN-----\n+--GGTILAMFTTAGFSTLFIGFFLSTIILYHATFSINSIMHKFGNQRYET\n+GDESRNSVWLALLTLGEGWHNNHHYYETSARQ-G-FFWWEVDLTYYGLKF\n+MSMLGLIWDLKPVPKHIKKSRNKQ--EAKELKEQFKKQVA---\n+>485918.Cpin_3312\n+------MNSEKQLRKGPNWWRQFDFLGLHLLPILAFWTHVTTFDWILCAV\n+LYVVRMFFVTGGYHRYFSHRTFKTSRFFQ---FILAGGAQSSLQKGVLWW\n+GANHRVHHKHSDTPEDPHSANIYGFWYAHMGWIM---GPEFKPTRYELIK\n+DFK-Q---PELYWLNK--------YHWVPGVILGVACYFIGNKVN-----\n+--GEGWFDWH--AGLSTLLVGFVLSTIFLYHGTFTINSLMHKWGKPRYKT\n+GDFSKNSAILALVTLGEGWHNNHHYYQSATRQ-G-FFWWEFDITYYILRT\n+LGVFGIVWDIRGVPEKVKSSNLLTDEAREEVKAANRRLVEENR\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,636 @@\n+>269798.CHU_2721\n+-----------------------------MNKINVLFVCLGNICRSPMAE\n+GIFRKIV-EKNNLQEHFQIDSSGTSRYHIGEHPDVRAIQTCKEKNIVLN-\n+HLGQEF-I-AEDFMNQDYIIAMDASNLSNIKALMSA------T-KMRAEI\n+FLMRD-FDL--Q-HAGANVPDPYYGGQEGFYEVFDMLERSSYELLHYIRS\n+KHSI-----------------\n+>880070.Cycma_1828\n+-------------------------------MIKVLFICLGNICRSPLAE\n+ALFNHKI-KQKGYEDYLCCDSCGTSDYHIGELPDERTMASAAKNGIKI-N\n+HRGRQL-N-RTDFRDFDYLIAMDDSNILNIKQA---A---DLHKTTVNNL\n+FLMRS-FQK-N--AAFSEVPDPYYGGVDGFQKVYEILDSSLDGFIESLEK\n+NHPEIGQK-------------\n+>388413.ALPR1_04493\n+-------------------------------MIKVLFVCLGNICRSPLAE\n+AIFDAKI-KKAKLPSAFKSDSAGTSDFHIGELPDERTISIAKKYNLPI-Q\n+HRGRQV-N-RTDFRDFDYILAMDDHNLRNLNNM---K---ARCGFDEKEI\n+FLIRD-FVP-G--TKGQSVPDPYYGGEEGFEEIYTILDEALDHFLAQIKE\n+THQLYV---------------\n+>679189.HMPREF9019_1834\n+---------------------------MKINKKKLLFVCLGNICRSPAAE\n+GVMKSIID-ANKANANYEVDSAGIGNWHVGQLPDSRMRACGLKRGYVFN-\n+SHARQF--TKSDFQYFDYIFVMDQENYRQITSQT------QN-EDERKKV\n+LMLADYITQ-P--ANVKIIADPYYGNEKDFNNALDLIEDACQQLFVALET\n+HNKSTNVI-------------\n+>575615.HMPREF0670_00803\n+--------------------------MEDRKRTKLLFVCLGNICRSPAAE\n+GVMKQVLL-NKGMSDLFEVDSAGIGGWHVGELPDSRMRKCGAARGYNFN-\n+SRARQF--DTDDFRKFDYIFVMDNDNKNMLSQKT------NN-ERELAKV\n+KMLVDYAAS-H--PKAKLIPDPYYGDEKDFDYALDLIEDATNTLADRLAK\n+GGEL-----------------\n+>619693.HMPREF6745_2163\n+--------------------------MEDKIRTKLLFVCLGNICRSPAAE\n+GVMKQVLL-NRGMTDMFEVDSAGIGGWHVGELPDSRMRKCGAARGYDFN-\n+SRARQF--STSDFKRFDHIFVMDNENWKMLSQKT------ND-QHELTKV\n+KMLVDYTTN-H--PKAKLIPDPYYGDEKDFNYALDLIEDAANGLADKLAE\n+GSEI-----------------\n+>679190.HMPREF0650_0583\n+---------------------------MNKMKKRLLFVCLGNICRSPAAE\n+GVMKSIVK-AAGMEDEFVIDSAGIGDWHIGQLPDHRMRKHGAQRGYRFD-\n+SRARQF--NADDFANFDHIYVMDHENKRMITAMA------AT-KEDAQKV\n+EMLASYLKD-K--QNVDVVPDPYYGGDEDFKYALDLIEIACKELFSQLNR\n+K--------------------\n+>873533.HMPREF0663_11067\n+-----------------------------MKKIKLLFVCLGNICRSPAAE\n+GVMKHIVH-QAGADEMFYIDSAGIGDWHVGQLPDARMRRHGAARGYDFG-\n+SRARQF-K-RDDFKRFDCILVMDHDNLRMVNAMT------ND-EEDRRKV\n+HLLTEYLTE-H--HDAATVPDPYYGGSADFDYALDLIEDACRGLYHKLTI\n+SV-------------------\n+>537011.PREVCOP_04462\n+--------------M-LTLQTKKVSNMTKKGKHTVLFICLGNICRSPAAE\n+GIMKSLVE-KAGLQDEFEIDSAGIGGWHIGQLPDSRMRKCGAEHGYNFN-\n+SHARQF-Q-KSDFARFETIVVMDNENYRAITSMA------SS-ESDRKKV\n+VRMADFLTH-H--REYTTVPDPYYGDYSDFELVITLLEDACQGLLDSIIG\n+EG-------------------\n+>862515.HMPREF0658_0454\n+----------------------------MKEKKSLLFICLGNICRSPAAE\n+GVMKKKAE-EAGMADSLYIDSAGIGGWHIGELPDRRMRSHALHRGYILD-\n+SRARQF-A-LPDFHNFDYIVVMDDENYRAILSLA------TD-EMEKNKV\n+WKMRDFFTK-Y--KGIADVPDPYYGSDAEFNRALDLIEDGCEGLLTHLFR\n+Q--------------------\n+>752555.PBR_1794\n+---------------------------MKKGKITVLFICLGNICRSPAAN\n+AVLQKMVD-DAGLTDRFLIDSAAVGPWHIGDLPDKRMRQAGAQRGWDIS-\n+HIARQF-DASSDFDRFDYIVVMDEENYKNITRQA------HH-EKERNQV\n+IRMADYFEH-H--PTYSTVPDPYYGGMADFELALDLIEDGCQGLLKQLFT\n+GK-------------------\n+>585502.HMPREF0645_0680\n+--------------------------MIKKGKVRILFICLGNICRSPAAQ\n+GVMQQMVD-DRGLAHRFSIDSAGIGGWHTGNLPDVRMRRHGKMRGYDFS-\n+HRARQF-DAATDFDEFDLIVTMDEQNHRDITRMA------AG-DDDRKKV\n+VRMSDYLKA-H--PDATSVPDPYYGGEQDFELALDLIEDGCENLLKELVC\n+TN-------------------\n+>702438.HMPREF9431_01007\n+------------------------MTTKNEAQTKILFICLGNICRSPAAH\n+AVFQKAIE-ERGLTHHYMVDSAGIGDWHVGQLPDKRMMLQGKKRGYCIN-\n+HHARQF-T-NDDFQHFDYIVVMDDDNYRIISQRA------RN-EAERKKV\n+MKMADFFQE-Y--KGVKSVPDPYYGTTRDFDNALDLIEDGVNGMLSRLV-\n+---------------------\n+>888832.HMPREF9420_2252\n+------------------------MNTKTASRTKILFICLGNICRSPAAH\n+AVFQQKIN-DKGLADRFEVDSAGIGNWHVGQLPDSRMRRQGERRGYMIN-\n+HKARQF-Q-TSDFKLFDRIVVMDNDNYRIIVSKA------SS-DEEAQKV\n+IRMADFFTS-H--PRATSVPDPYYGGPEDFDLALDLIEDGVEGLLKDMMK\n+A--------------------\n+>563008.HMPREF0665_01100\n+------------------------MNSKTAARTKILFICLGNICRSPAAH\n+AVFQKKID-DRGLSERFEVDSAGIGNWHVGQLPDRRMREYGARRGYQVN-\n+HHARQF-Q-TSDFKHFDRIVVMDEDNYRIITSKA------SS-DEEAGKV\n+VRMADFFTS-H--PRATSVPDPYYGGAEDFELALDLIEDGVEGMLKEMGE\n+E--------------------\n+>575611.HMPREF0649_00334\n+-----------------------MGKIQTKDKTNLLFICLGNICRSPAAH\n+AVMQKMVD-ERGLGDTFEIDSAGIGDWHVGQLPDRRMREHGSRRGYRFD-\n+HRARQF-DPHEDFARFDHIIVMDEENYRNVT'..b'--------MVCLGNICRSPLAE\n+GILKSKL-PD-----TYLIDSAGTGGWHAGEQPDKRSIQTARNKGIDISQ\n+QRARKF-K-KLDFDFFDCIFVMDNQNYKDVINQ---A---ST-ENQKNKV\n+QLILD-EIF-P--NEKVDVPDPYYGGQEGFEQVFNMLEQACQSIADRLKK\n+SL-------------------\n+>391598.FBBAL38_08699\n+------------------------------MASKILMVCLGNICRSPLAE\n+GIMRSKL-SK-----DFIVDSAGTGGWHAGELPDKRSISTAKNKGLDITN\n+QRARQF-K-KSDFDTFDHIFVMDNSNYKDVLAL---A---PN-EEAKSKV\n+KMILN-EIF-P--NENVDVPDPYYGGQDGFENVYNMLDQACEEIARKLK-\n+---------------------\n+>867900.Celly_0002\n+-------------------------------MTKILMVCLGNICRSPLAE\n+GILKNKV-DPT----IISVDSAGTAGYHIGSAPDPRSVAVAKKYGIDISK\n+QVCRKF-T-VKDFDEFTTIYVMDNSNYNNVIAL---A---KT-PEHKKKV\n+KLLLH-FAD----TKITEVPDPYYGGDQGFENVYNLIDQACTNIAKTLKN\n+Q--------------------\n+>313603.FB2170_13483\n+------------------------------MATKVLMVCLGNICRSPLAE\n+GILQSKV-DSD----VVIVDSAGTGGYHIGSQPDSRSISVGLKYKIDIRN\n+QRCRKF-I-PNDFEDFDLIYVMDKSNYANVIAQ---A---NH-NHEIVKV\n+RLLLN-ELG-P---GDKEVPDPYYD-DDGFEHVFNLIDEACEVIANNLNS\n+N--------------------\n+>391587.KAOT1_08428\n+------------------------------MKTKILMVCLGNICRSPLAE\n+GILASKL-DPT----KFEVDSAGTAGYHVGELPDRRSIATAKQHGLDISY\n+QRSRKF-T-KNDFQTFDYIFAMDKSNYDNILAL---A---ET-AEDRAKV\n+HLILN-QIS-P--NSNAEVPDPYYGGDQGFENVYQMLDKACSIFAERIS-\n+---------------------\n+>313598.MED152_13409\n+-------------------------------MTKVLMVCLGNICRSPLAE\n+GILQSKI-NTD----TIFVDSAGTAAYHVGNLPDERSIAVAQKYGIDITN\n+QRARKF-T-SKDFDEFDFIYAMDESNYQNIVSL---A---RN-SEDEKKV\n+HLILN-ESQ-P--NQNLSVPDPYYGGKDGFENVYQMLDEACTVIASKL--\n+---------------------\n+>886377.Murru_0002\n+------------------------------MKTKVLMVCLGNICRSPLAE\n+GILQSKV-DSD----SVFVDSAGTAGYHVGNPPDERSIAVARKYGLRIEG\n+QKCRKF-S-QQDFLEFDHIYVMDRSNFSDVASL---A---KN-KEEASKV\n+KLLLS-EIE-L--GIK-EVPDPYYGGDDGFENVYQIIDSACEVIAKKLN-\n+---------------------\n+>313596.RB2501_16104\n+------------------------------MATRILMVCLGNICRSPLAE\n+GIFASKL-AGE----DYVVDSAGTAGYHVGNPPDPRSIEVAAQYGIDISR\n+QRCRRF-S-VSDFDNFDYIFAMDLENQANILSL---A---RN-ERDRAKV\n+SLLLE-AGG----KGRREVPDPYYGGADGFEQVYRMIDTACDYILAEYIG\n+KPDGKK--S------------\n+>156586.BBFL7_00667\n+-----------------------------MSKTSILMVCLGNICRSPLAE\n+GIMRSKL-NFT----KFNIDSAGTSGSHRGQAPDKRSIAVAKKNGLDISS\n+QASRKL-V-VEDLVKFDYIFVMDNSNYRDVIAL---A---EN-DEQRAKV\n+HKIMD-WAF-P--NEDLDVPDPYYGGDSGFENVYRMLDHVSNVIAKKLDS\n+LTNL-----------------\n+>391603.FBALC1_10232\n+-------------------------------MTRILMVCLGNICRSPLAH\n+GILQSKL-SEN----HFYVDSAGTAAYHIGKKPDYRSVEVAKKYNLDISK\n+QKARQF-K-ARDFDSFDYIFAMDQSNYSNIISL---A---RD-NRDIGKV\n+KLFLE-DNT-S--IINKNVPDPYYGDDDGFERVYTLIETTCELIAQKLLS\n+NTG------------------\n+>860228.Ccan_08390\n+-----------------------------MGKTKILMVCLGNICRSPLAE\n+GVLRSKL-NAE----LFEVDSAGTSNYHVGDAPDHRSVEVARKNGIDISN\n+LRGRQF-Q-TSDFEYFDYIFVMDESNYENVLKL---A---KT-SQHREKV\n+SLLLD-VFD-S--EVKREVPDPYYGGKNDFQAVFTLIDGACNAIAEKLNA\n+---------------------\n+>888059.HMPREF9071_1449\n+----------------------------MIPSTRILMVCLGNICRSPLAE\n+GVLRSML-DKD----FFEVDSAGTAGYHIGQAPDNRSILVAKKYGIDISS\n+LKGRIF-T-PEDFDKFDYIFVMDKSNYKDILSL---A---KS-EKQ----\n+--------------------------------------------------\n+---------------------\n+>706436.HMPREF9074_06136\n+-----------------------------MKKTKILMVCLGNICRSPLAE\n+GVMRSKL-PID----SFEVDSAGTANYHIGDAPDPRSIASGKKHGVDISM\n+LRGRQF-S-ITDFEAFDYIFVMDRSNYQYLIRL---A---RN-EHDLNKI\n+SFLSD-ALD-K--MTKAEIPDPYYGSEADFEKVYQLIDAACEKVAHKLTT\n+NS-------------------\n+>553177.CAPSP0001_1409\n+-----------------------------MPKTKILMVCLGNICRSPLAE\n+GVMRSKL-PSD----NFEVDSAGTANYHVGDAPDDRSIASGKQHGIDISM\n+LRGRQF-S-AKDFSHFDYIFVMDRSNYQNVIRL---A---KN-EKERAKV\n+HFLAD-ALG-G--MAQREIPDPYYGTEADFENVYQLIDEACTKVAHKLSN\n+-P-------------------\n+>873517.HMPREF1977_0850\n+-----------------------------MKKTKILMVCLGNICRSPLAE\n+GVMRSKL-PSD----NFEVDSAGTANYHVGDAPDTRSIASGKKHGVDISM\n+LRGRQF-S-AKDFALFDYIFVMDKSNYQNVIRL---A---KN-EKERAKV\n+HFLAD-ALG-G--MTQHEIPDPYYGTEADFENVYQLIDKACTKVAHKLSP\n+NP-------------------\n+>521097.Coch_2170\n+-----------------------------MKKTKILMVCLGNICRSPLAE\n+GVMRSKL-PSD----NFEVDSAGTANYHVGDTPDTRSIASGKKHGVDISM\n+LRGCQF-S-AKDFALFDYIFVMDKSNYQNVIRL---A---KN-EKERAKV\n+HFLAD-ALN-G--MTQHEIPDPYYGTEADFENVYQLIDEACTKVAHKLSP\n+NP-------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,155 @@
+>908937.HMPREF9136_0707
+--------------MMDTLTYFQSDRFINHIDARLVEAHEGYAKAVMTVA
+EHHLNGYGVCQGGALFTLADLAFAAAVNSHGISTLTTNASITYVKSARLG
+DRLTAEGHEVVNHHKMPFAEVRVCNQ------HQELLAVFTASGYRKEKH
+GERKG-------------
+>547042.BACCOPRO_03519
+--------------MKTLKELLAKDHFAANAGVELLEVSPGYARARMLVT
+VKHLNAGGVCQGGALFTLADLAFAAVANSHLKLTLSLNANITFLRSAHEG
+-YVYAEATETFSHARVPFIEVRITDD------EGQLVAIFTSSGYRKNEE
+LPVETLK-----------
+>585543.HMPREF0969_01459
+---------------MTAQEFFKNDRFATNAGVELIEIKEGYSKARLVIT
+AEHLNAGGRTQGGAIFTLADLALAAAANSHGTLAFSLSSNITFLRSSGPG
+DVLYAEARERYIGRTTGYYQIDVTNQ------EGKLIATFESSVFRKGDN
+ITFSLPQTSSDSGCPGHS
+>272559.BF0160
+---------------MTAQEFFKNDLFATNAGVELIEIREGYSKAKLEIK
+PEHLNAGQRTQGGAIFTLADLALAAAANSHGTLAFSLSSNITFLRASGPG
+DTLYAEARERYTGRSTGYYQIDVTDQ------EGRLIATFESSVFRKKDE
+VPFTL-------------
+>457424.BFAG_02844
+---------------MTAQEFFKNDLFATNAGVELIEIREGYSKAKLEIK
+PEHLNAGQRTQGGAIFTLADLALAAAANSHGTLAFSLSSNITFLRASGPG
+DTLYAEARERYTGRSTGYYQIDVTDQ------EGRLIATFESSVFRKKDE
+VPFTL-------------
+>483215.BACFIN_08066
+---------------MTPQEFFKNDIFATKAGIVLLEVRKGYSKAKLDIK
+PEHLNAGARTQGGAIFTLADLALAAAANSHGTLAFSLSSTITFVRASGPG
+DTLYAEAHERYIGRSTGCYQVDITNQ------NGDLIATFESSVFRKEQK
+VPFEIEKEK---------
+>411476.BACOVA_01979
+---------------MTAQEFFKNDLFAENAGVVLLEVRKGYSKAKLEIK
+PEHLNAGARTQGGAIFTLADLALAAAANSHGTLAFSLSSTITFLRASGPG
+DTLFAEARERYIGRSTGCYQVDITNQ------DGELIATFESSVFRKDQK
+VPFEVQE-----------
+>657309.BXY_26270
+---------------MTAQEFFKNDLFAENAGVVLLEVRKGYSKAKLEIK
+PEHLNAGARTQGGAIFTLADLALAAAANSHGTLAFSLSSTITFLRASGPG
+DTLFAEARERYIGRSTGCYQVDVTNQ------NGDLIATFESSVFWKDQK
+VPFEVQE-----------
+>226186.BT_3343
+---------------MTPQEFFKKDLFAENAGVVLLEVREGYSKAKLEIK
+PEHLNAGARTQGGAIFTLADLALAAAANSHGTLAFSLSSSITFLRASGPG
+DTLYAEARERYIGRSTGCYQIDITNQ------NGDLIATFESSVFRKDQK
+VPFTL-------------
+>411901.BACCAC_01535
+---------------MTPQEFFKNDLFAENAGVVLLEVREGYSKAKLEIK
+PEHLNAGARTQGGAIFTLADLALAAAANSHGTLAFSLSSNITFLRASGPG
+DTLYAEAHERYIGRSTGCYQVDVTNQ------NGDLIATFESSVFRKEQK
+VPFEIQK-----------
+>449673.BACSTE_02469
+---------------MTPQEFFKKDCFADKAGVELIEIKEGYSKARLVIT
+ETHLNAGNRTQGGALFTLADLALAAAANSHGTLAFSLSSNITFLRSSGPG
+DILYAEARERYIGRTTGHYQIDITNQ------NGELVATFESSIFRKGDA
+LPFTL-------------
+>483216.BACEGG_03405
+---------------MTPQEFFKKDRFADNVGVELIEIKEGYGKARLVIT
+EEHLNAGNRTQGGALFTLADLALAAAANSHGTLAFSLSSNITFLRSSGPG
+DTLYAEARERYAGRSTGYYQIDITNQ------KGELVATFESSVFRKGDA
+LPFAVPL-----------
+>762984.HMPREF9445_00029
+---------------MTPQEFFKKDLFAGKTGVELIEIKEGYSKARLVIT
+EEHLNAGHRTQGGALFTLADLALAAAANSHGVLSFSLSSNITFLRGSGVG
+DTLYAEARERYVGRTTGYYQIDVTNQ------KGELIATFESSVFRKGDA
+LPFTL-------------
+>763034.HMPREF9446_01296
+---------------MSPQEFFKKDYFAEKVGVELLEIKEGYSKARLVIT
+EEHLNAGHRTQGGAIFTLADLALAAAANSHGTLAFSLSSSITFLRGSGPG
+DILYAEARERYTGRTTGYYQIDITNQ------EGKLIATFESSVFRKEDK
+LPFTVGKGGK--------
+>471870.BACINT_01375
+---------------MTPQEFFKKDLFAEQTGVELLEVREGYSKACLVIT
+ENHLNAGHRTQGGAIFTLADLALAAAANSHGSLAFSLSSNITFLRASGPG
+DTLYAEARERYIGRTTGYYQIDITNQ------DGKLIATFESSVFRKGDP
+LPFSV-------------
+>531844.FIC_02223
+-----------MSPHELAQYILSQDHFSQWMGIKLIEVREKYCLIEMPVK
+QEMINGLRTVHGGVTFSLADSALAFSSNNTNDASVALHCAMNFAKAVKLG
+DTLTAESILISDTRKTGVYDISITNQ------HKVLVASFRGTVYKIDKK
+VTDL--------------
+>525257.HMPREF0204_10054
+-----------MNPRQVADYMFNQDYFSQWMNIRMIEVKENYCLIEMPIK
+KDMLNGLKTVHGGVTFAFADSALAFSSNNTGDAAVALNCIINFTKAGKAG
+DVFRAESVLVNDTRKTAVYDIQITNQ------NSELIAKFVGTVYKIGKK
+VTDL--------------
+>518766.Rmar_1553
+MPAQADNETAEQRARQIVDQMMARDAFSRWLGIEVLEVTPGRAVVRMTVR
+PEMLNGFAVAHGGIAFALADSALAFASNTCGMVTMTLESSIFFATPVRAG
+DVLTATAEETSAGNRVALYDVVVTRA------DGTRVAFVRGTAYRTKQA
+HD----------------
+>755732.Fluta_2450
+---------M-KTPQDIVTEMMNTDAFSQWLGIRILEIEPGFCKLTITVR
+PEMVNGHQTAHGGISYSISDSALAFAANSRGQKAVSIETSIAHIAPVFVN
+DELLVICKEINCGKTIGRYESIVYNQ------NQKIIAKFNGTVFRHPEL
+W-----------------
+>313595.P700755_04128
+-----------MKPTTIPEKMLSQDAFSSWLGVEILEISLGKCKVGLKIR
+REMLNSMQKAHGGITYSLADTAFGFAANTHGNYAVSIETSINHIEALHEN
+DYITAESIVEVTKNKLGFHIVELKK-------GEQIVALFKGVVYRTSKE
+WE----------------
+>1034807.FBFL15_1504
+-----------MNSSTIPHKMLSQDAFSQWLGITILESEIGKCKVGMTVR
+KDMLNSMGKAHGGITFALADTAFGFAANALGKYAVSIETSINHIEAVSEG
+DYLTAVSVIEKSKNKLGFHIIEVRRHTANNQEPDELVALFKGVVFRTQKD
+WEI---------------
+>156586.BBFL7_02456
+-----------MDGKKIPAKMLSLDPYSTWLGIEILSVEIGSVKLGMTIR
+PVMLNSMGKAHGGITYSLADTAFGFSSNTHGKFAVSIETSINHIEALVEG
+DYITAECTLDKTKTKVGFNIVEVKK-------GDELVALFKGVVYRTNKD
+WEN---------------
+>391587.KAOT1_20537
+---------MPISGEKIPTKMLSQDPFSTWLGIEILECEIGRCKVGLTIK
+KDMLNSMGKAHGGISYSLADTAFGFAANTHGKYAVSIETSINHIEALEEG
+DFITAESVIEKVKNKLGFNIVEVKR-------GDELIALFKGVVYRMQKD
+WEE---------------
+>391603.FBALC1_14212
+-----------MKGEAIPYKMLSQDAYSQWLGIEILECEIGRCKVAMTIR
+KEMLNSMSKAHGGISYSLADTAFGFTANTHGKYAVSIETSINHIEALEEG
+DYLVAESIIEKVNNKLGFNIVEVKR-------GDELVALFKGVVYRTQKD
+WEE---------------
+>1046627.BZARG_1573
+----------------------------------------------MTIR
+KDMLNSMNKAHGGISYSLADTACGFAANSHGKYAVSIETSINHIEALNEG
+DYIVAESVIESVKNKLGFNIIEVKR-------GDELVALFKGVVYRTSKD
+W-----------------
+>983544.Lacal_1616
+---------MPLTGDQIPHKMLSQDAYSTWLGIEILECEIGRCKVAMTVR
+KEMLNSMGKAHGGISYSLADTAFGFAANTHGKYAVSIETSINHIEALEEG
+DYLTAESVIENVKNKLGFNIIEVKR-------GEELVALFKGVVYRTSKS
+WEE---------------
+>216432.CA2559_05295
+---------MPISKTKIPNKMLSQDHFSSWLGIEIISVEIGRVKVGMTIR
+KEMLNSMGKAHGGISYSLADTAFGFSANTHGKYAVSIETSINHIEALEEG
+DYITAEAVTDVSKKKVGFNIVEVKR-------GDQLVALFKGVVYRTSKD
+WE----------------
+>313590.MED134_11701
+-----------MTGAQIPYKMLSQDAYSSWLGIEIIEAQVGFVKVGMTIR
+KEMLNSMGKAHGGISYSLADTAFGFTANTHGKYAVSIETSINHIEALEEG
+DYITAEATVNLQKTKVGFNIVEIKR-------GDELVALFKGVVYRTSKD
+WEID--------------
+>50743.SCB49_08393
+MPNTK--SLGPLAGERIPHKMLAQDAYSTWLGIEILDCKVGHVKVGMTIR
+KEMLNSMGKAHGGISYSLADTAFGFTANTHGKYAVSIETSINHIEALNEG
+DFITAEATLDLQKNKVGFNIVEVRR-------GDELVALFKGVVYRTNKD
+WEE---------------
+>926562.Oweho_2251
+-----------MEGKAIVDKMYNGDAFSQWLGIERIEERAGYSKLKMRVR
+EEMTNGFKIAHGGITYSLADSALAFASNSHGRQAVSIETSISHTKAVHIG
+DILIAEAIELNLTNATGIYDIKVTNQ------NNEVVALFKGTVYRTKKE
+WTN---------------
+>700598.Niako_6202
+M------SDSKSKTTAIVDAMMGKDYFSQWLGIERLEEKEGFCKLRMTVR
+KEMCNGFEMAHGGISYSFADSALAFASNSHGRHAVSIETSISHIKPLKTG
+DVITATAEEKSRGNKIAIYDVRVEKE------SGELVALFKGTVFRKETE
+WNV---------------

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,340 @@\n+>411476.BACOVA_04627\n+------------------MLNKALNIAYKAHIGQLDKGGSPYILHP----\n+-----------V-----RVALHCQTEDEKIVALLHDVVEDTSITFEDLKT\n+EGLDDRLLEALKCLIKEEGEDY-------KAFIERV-STNRLATKVKIQD\n+LKDNMDVTRLNGKAHWKLETYKEALEYL--------------------E-\n+------RCSNKKV--LYVDMDNVLVNFQSGI---DALN--E---------\n+-DLKSRY----------AGCYDEVPNIFAKM--------QPNEGAIDAMN\n+RLK--DKYDIYILSTAPWDNPSAWSDKLEWVKRYLGEVCYKRLILSHHKN\n+LNAGDYLIDDRKKNGAADFKGELILFG-------SERFPNWESVVRYLL-\n+------\n+>657309.BXY_30930\n+------------------MLNKALNIAYKAHIGQLDKGGSPYILHP----\n+-----------V-----RVALHCQTEDEKIVALLHDVVEDTSITFEDLKT\n+EGLDDRLLEALKCLTKEEGEDY-------KAFIERV-STNRLATKVKIQD\n+LKDNMDVTRLNGKAHWKLETYKEALEYL--------------------E-\n+------RCSNKKV--LYVDMDNVLVNFQSGI---DALN--E---------\n+-DLKSRY----------AGCYDEVPNIFAKM--------QPNEGAIDAMN\n+RLK--DKYDIYILSTAPWDNPSAWSDKLEWVKRYLGEVCYKRLILSHHKN\n+LNAGDYLIDDRKKNGAADFKGELILFG-------SERFPNWESVVRYLM-\n+------\n+>657309.BXY_06030\n+-----------------------M-------ISALSTF------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------KPI--LYIDMDNVLVDFQSGI---NKLS--E---------\n+-YEKKEY----------EGRYDEVPNIFAKM--------YPYKGAIDAFH\n+RLV--RFYDVYILSTAPWNNPSAWSDKLVWVKKWLGTYSYKRLILSHHKN\n+LNKGDFLIDDRLKNGAENFSGELILFG-------SEQYPNWDSVVDYLI-\n+-S--SK\n+>1034807.FBFL15_2516\n+-----------------------M-------------K------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------KKI--LYLDMDGVVADFEQSV---LHICPEL---------\n+-NTATQYENP------KKRDAKIDQICATELDFFHNL--LPMKGAVEAVS\n+QLF--PLYDLYFLSSPMWGVPESYIGKRIWIEKHFGVLAKKRLILSHRKD\n+LHLGDFLVDDRTRNGAGEFQGFHIHFG-------TEQFPDWETTLAFLI-\n+-E--NI\n+>983544.Lacal_2144\n+-----------------------M--------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------KKI--ILIDMDGVLVELGDGP---FSEN--K---------\n+----------------------HKKGFFLNN--------KPIKGAVEAFK\n+VLS--KKYDCYIVTAPVWSNPNCWKEKRLWVEKHLGDDANKRLILTHNKN\n+LVKGDYIIDDTKNYGVDKFEGKHIMFG-------NDLYPNWKKVLEYFI-\n+-D---K\n+>313594.PI23P_04607\n+-----------------------M----------IKTT------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------KKI--VFIDMDGVLVDFKDAIENAYRIN--P---------\n+-KYKEKF----------KNNPDEIKGIFKNP--------KPIDGAIDAVI\n+KLANSGRYNLFIATTTPWENPKAAMHKRLWIEKHFGDLFLKKMFITHRKD\n+LLIGDYLIDDRLKNGASEFRGELLSFGWAYEQNQWNEYKTWGDILKKLL-\n+------\n+>313595.P700755_04872\n+-----------------------M-------------E------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------KPI--VFIDMDGVLADLGAGA---KASP--L---------\n+-FQEDQY----------KNDPDDIPDIFENL--------PPIKDAIEAVN\n+KLHDTKRFDLFILTTAPWDNPSAWMHKRTWIEKHFGDKFYQKIIITHRKD\n+LLIGDYLIDDRTARGASEFKGKHIHFGWDYVNQKDNEYPNWESVLEFFD-\n+-C--N-\n+>679937.Bcop_1455\n+------------------------------------MENKIIYVHGLSSS\n+GATASAQNIQALLPQYQVVAP-------------------------DMPL\n+P--PQQALQLLTDLVAELQPVLVVGTSMGAMFTQQLHGQTKILINPAFHV\n+-SQLMRKN--LGTQPFFNPRKDGVMTFDITPQLCDAYEIMEKHQFDKVT-\n+------VYDQEHTYGFFGTHDEMVNCQEEFS---RYYPHKVLFEGEHRLN\n+PEVIERDLVPLIQSI-----------------------------------\n+-LMN----------------------------------------------\n+--------------------------------------------------\n+-----S\n+>575614.HMPREF0669_00681\n+------------------M-----QTSQLNNASNLMAGKKVLYVHGFMSS\n+AQSGTVHLLKELMPQAEIIAE-------------------------DLPL\n+H--PQEALDMLRELCKSEQPDLIIGTSMGGMFTEMLYGYDRIVVNPAFRM\n+-GETMSKHGHMGKQVFQNPRKDGVQEFIVTKALVKEFDEVTAQCFTQVT-\n+------NDEQQRVYGLFGDEDEFVTCSDLFE---QYYTNSISFHGGHRLT\n+DKVALHSLLPVIRWIDNKQEQREPPVVYISYETLLDAYAKPKSSLMKAYE\n+MLLV--NYNVVIVVPSAPYHPEITAEKQQWIEQYLSVPAYKHVVLCDDIS\n+LLYGDYLITTNE---DAPFLGTVITFGS-----'..b'----M-----DNPYSKQFPSLMKGKKIMYVHGFLSS\n+AQSGTVKMLQELMPKSSVIAE-------------------------DIPV\n+H--PEEAMQMLRKMADNEQPDLIIGTSMGGMYTEMLHGFDRILVNPAFAM\n+-GDTMS--SMTGHQEFQNPRKDGVQDLMVTKGLIKEYKDMTTQCFANID-\n+------TEERERVYGLFGDNDPVVHTFDLFR---QHYPNAIYFHGEHRLI\n+DKVALHYLIPVIQWIDDRQNGTERPIVYLHFDALHDSFGKPLSSMHKAYE\n+LLLE--HYQVYIVAPVPTNNHAYTEEVQHWTEEFFSAPAYNHVIFTNQKN\n+LLYGDYFIDPKP---HPDFMGTTIAFGN-------DEFKTWEEVITFFER\n+LG--GQ\n+>873533.HMPREF0663_10155\n+------------------M-----ENQYIKQYSDIMSGKTILYVHGFGSS\n+AQSGTVKRIQDTLPQSKVVAY-------------------------DLPL\n+H--PEEAMSLLRRVCSEQNPGLIIGTSMGGMYTEMLYGYDRIIVNPAFRM\n+-GETMHEHGMMGKQTYQNPRQDGIQEFIVTKALVKEYKEITEQCFAHVTA\n+-------EERNRVYGLFGDQDQVVHTFDLFH---EHYPNAIRFHGEHRLT\n+DKSFFHSVMPVIRWIDDRQEGRERPIVYIHDNTLRDAYGKPKSSLNKAYE\n+FLIE--KYDVYIVVPAPTNNHPMIDAAQTWTENILGTPAYDRVIFCNQRR\n+LLYGDYFIDAAP---CKEFMGTTITFGS-------DDFKTWEDVIVFFER\n+LGG--Q\n+>575611.HMPREF0649_00924\n+------------------M-----ENPYIKQFPDLMSGKTIMYVHGFGSS\n+AASGTVKRIRETLPSARVVAY-------------------------DLPL\n+H--PEEAMALLQEKCAEERPALIIGTSMGGMYAEMLRGYDRILVNPAFEM\n+-GDTMHEHGMMGKQVFQNPRQDGVQEFIVTKALVKEYRDITARCFAGITD\n+-------DERRRVWGLFGEEDPVVHTFDLFR---SHYPQAVHFHGEHRMT\n+DKSFLHGVLPVIRWVDDRQESRERPIVYLHWNTLADSYGNPKSSLNKAYD\n+LLVE--RYEVYVVVPAPTNDHASLTAAQEWIERYLSTPAHDRVVFANQKA\n+LLYGDYFIDSEP---CKDFMGTTLAFGS-------DDFKTWEEVIVFFER\n+LGG--Q\n+>688246.Premu_0566\n+----------------MEK-----DNPYIKQYPDLMQGKKMMYNHGFGSA\n+ASSGTVKLIRQTFPNAEVVAY-------------------------DIPL\n+H--PAEGLALLKEKAEVEKPDLIIGTSMGGMYTEMLYGFDRICVNPAFEM\n+-AQTMKEHGLTGKQTWQNPRQDGETEFMVTKALEKEYKEMTDQCFTAMEA\n+MTAEEKAKELQHVWGLFGDEDDVVNTWDVFC---SHYVQAAHFHGAHRMD\n+DKSFLAGVVPVIRWIDDRQEGRERQIVYIDSSCLADSYGKPRPSLHKAFS\n+TLVE--KYQVYIVVPAPTNSHDSFAQNAEWIERYLSTPAHDHVIYTNQKQ\n+LLYGDFFIDMRP---ADNLLATAIQLGS-------DEFKTWEEVITYFSR\n+I-----\n+>585502.HMPREF0645_0469\n+------------------M-----DNPYIKQFPDLMNGKTIMYNHGFGSS\n+AATGTVARIRQVFPHARVVAF-------------------------DIPL\n+H--PEEALDFLKKKAAEERPDLIIGTSMGGMYTEMLYGYDRILVNPAFQM\n+-GQTMKDHGMTGMQTWQNPREDGEKEFIVTKALEKEYKEMTERCFVELEA\n+MTPEQKTEEQRRVWGLFGDADPVVHTFDLYR---SHYPQAAHFHGEHRMD\n+DRSFMNGVVPAIRWIDDKQEGRERHIVYIDQSTLCDGWGKPASSLVKAFS\n+MLVE--TYDVYIVMPAPTNEHETFAANAAWVEQYLSTPAHDRVIYTNRKH\n+LLYGDYFIDTNP---CEEFMGTGIAFGS-------DEFKTWEEIITFYKR\n+LNG--Q\n+>908937.HMPREF9136_1072\n+------------------M-----ENPYVKQFPDLMAGKIILYNHGFGSS\n+AASGTVARIRQTFPQARVEAF-------------------------DLPI\n+H--PAEAMDLLRRKVDELKPRLILGTSMGGMYTEMLYGYDRICVNPAFEM\n+-GQTMKDHGMTGKQLWQNPRRDGETGFLVTKALEKEYREMTEQCFNALEA\n+MGPEARAAEQQRVWGLFGDEDDVVDTYALYR---RHYPQAARFHGGHRMD\n+DRSFMNGVVPVIRWIDDRQEGRERPIVYIDSSTLADGYGKPKSSLAKAFA\n+LLVE--SYEVYVVAPAPTNAHADLADTASWVEQYLSTPAHDRVIYTNQKR\n+LLYGDYFIDTAP---DTGFMGTGIAFGS-------DEFKTWEDIITFYSR\n+LKPAES\n+>862515.HMPREF0658_1534\n+-------------------------MEYRKTFPDVMAGKKILYVHGFCSS\n+GQSGTVHLLRTLLPNTVVIAP-------------------------DLPL\n+H--PEEAMTLLRETCAIEKPDLVIGSSMGGMYAEMLYGFDRILVNPAFEM\n+-GDTMTHHGMLGKQQFLNPRRDGVQEFIVTKALVKEYKEITEQCFAKVD-\n+------EVERQRVTGLFGDKDPLVDTFELFN---SHYPNALHFHGAHQLL\n+DRVAVHYLVPVIRQIDDRQEKRERPVVYISPTALRDEAGKARPSMYKAYE\n+ALLE--HYRVYLVAPAPTNHHAAIGEFQCWTEEALSTPAHDHIVFTNCRS\n+LLYGDYLIDTTP---CTEFLGTVLLLGS-------DTFKTWDDLIVYFER\n+LGG--Q\n+>575615.HMPREF0670_01872\n+-------------------------MDPTKTYPALMKGKKIMYVHGFGSS\n+GQSGTVTLLRTLMPAATVIAP-------------------------DLPL\n+H--PAEALELLKQTCDAEKPDLIIGTSMGGMYAEMLRGTDRILINPAFEM\n+-GDTMVKHNMVGKQTFQSPRTDGIQDFIVTKALVNEYKEITTLLFNGID-\n+------EAEQQRVIGLFGDEDTSVDTFDLFA---QHYPTAIHFHGGHRLT\n+DKVAMHYLMPLIRQIDDKQTGRQRPIVFIHANTLADSYQKPMPSMHKAYE\n+MLIE--NYDVYILAPSPTNAPEQITAQMAWVEQYLNAPAFNRVVFCNNAN\n+LLYGDYLISRHE---HPNFLGSSILFGG-------NDLKTWDDVIVFFDR\n+LGG--Q\n+>619693.HMPREF6745_0609\n+-----------------------------------MKGKKIMYVHGFGSS\n+GQSGTVTLLRTLMPESTVVAP-------------------------DLPL\n+H--PAEALALLRQTCDIEKPDLIIGTSMGGMYAEMLRGTDRILINPAFEM\n+-GDTMVKHNMVGKQTFQNPRVDGVQDFIVTKALVNEYKEITTQLFNGID-\n+------ETERQRVTGLFGDEDTSVDTFDIFA---QHYPTAIRFHGGHRLT\n+DKVALHYLVPLIRQIDDRQTGRQRPIVFIDANTLADSYQKPMPSMHKAYE\n+MLIE--NYDVYILAPSPTNAPEHITAQMAWVEQHLNAPAFNRVVLCNNSN\n+LLYGDYLISRHE---HPNFLGSAILFGG-------NDLKTWDDIIVFFDR\n+LGG--Q\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1212 @@\n+>203275.BFO_3058\n+--------------------------------------------------\n+----------M-KKQKQGTVCVQGGWQ--PKNGEPRVLPIYQSTTFKYET\n+SDEMGKLFDLEASGFFYTRLQNPTNESVADKIASLEGGMAAMLTSSGQAA\n+VFYALFNICETGGHLICTSKIYGGTFNLLGVTMKKMGVDVTFIDQETTDE\n+EIEKAFRPNTKAVFGETLANPAGAVLDIERFARMAHSHGVPLVVDNTL-A\n+TPISCRPIEWGADIVVHSTTKYMDGHATAVGGAIIDSGNFDWSAHKDQFP\n+GLTTPDPSYHGIVYTEKFG--------KTAYLVKATVQLMRDFGSTASPM\n+NAFLLNIGLETLHLRIPRHCSNAQAVAEYLAGHPKVAWVNYCGLPENKYH\n+TLARKYLPEGSCGMLTLGLKGGR----DHAIRFMDALRLVSIVTHVADVR\n+SCVLHPASHTHRQLSDEQLVAAGVAPDLIRFSVGIEDIDDILADVQQALE\n+KA--------------\n+>435591.BDI_3768\n+--------------------------------------------------\n+----------MDNKFKPETLCVQAGWQ--PKKGEPRVLPIYQSTTFKYET\n+SEQMAKLFDLEESGYFYTRLQNPTNEAVAAKIAALEGGVAAMLTSSGQAA\n+SFFAFFNICEAGDHIVSATSIYGGTYNLLAVTLKKLGIECTFIDQDASEE\n+EISKAFRPNTKAMFGEMISNPGVMVLDVEKFARIAHNHGVPLIVDNTF-A\n+TPINCRPFEWGADIVTHSTTKYMDGHATSVGGCIVDSGNFDWEAHAEKFP\n+GLCQPDPSYHGLTYTKAFG--------KLAFITKATSQLMRDLGAIQSPQ\n+NAFLLNLGLETLHLRVPQHCKNALAVAQWLQKCDKVAWVHYPELEGNPYH\n+ELAKKYLPNGSCGVLSFGLKGGR----EVAIKFMDSLKLAAIVTHVADAR\n+TCVLHPASHTHRQLSDEQLIEAGVAPDLIRFSVGIENADDIIADIEQALN\n+K---------------\n+>706436.HMPREF9074_05505\n+--------------------------------------------------\n+----------MEKKLRRESVCVQAGWT--PKKGEPRVLPIYQSTTFKYDN\n+SEQMARLFDLEDTGYFYTRLQNPTNDAVAAKIAELEGGVGAMLTSSGQAA\n+NFYAVFNICQAGDHFVTSNTIYGGTYNLFGVTMKKLGIECTFVDPEWDDK\n+RIEAAFRPNTKCFFGETISNPGGHVFDIERFARMAHKHGVPLIVDNTF-A\n+TPINCRPFEWGADIVTHSTTKYMDGHATSVGGAIVDSGNFDWNAHADKFP\n+GLCQPDESYHGLTYADAFG--------KMAYITKATAQLMRDLGSIQSPQ\n+NAFLLNLGLETLHLRMRQHCANAQAVAEYLEQNERVAWVNYCGLKSNKYY\n+ELGQKYLPNGSCGVIAFGLKGTK----EDAIRFMDSLKMICIVTHVADAR\n+TCVLHPASHTHRQLSDEQLREAGVAPDLIRLSVGIENVEDIIEDIQQALD\n+ASK-------------\n+>762982.HMPREF9442_02276\n+--------------------------------------------------\n+----------MEKKLRKESVCVQAGWT--PKKGEPRVLPIYQSTTFKYDN\n+SEQMARLFDLEDTGYFYTRLQNPTNDAVAAKIAELEGGVGAMLTSSGQAA\n+NFYAVFNICQAGDHFVTSNTIYGGTYNLFGVTMKKLGIECTFVDPEWDDE\n+RIEAAFRPNTKCFFGETISNPGGHVFDIERFARMAHKHGVPLIVDNTF-A\n+TPINCRPFEWGADIVTHSTTKYMDGHATSVGGAIVDSGNFDWNAHADKFP\n+GLCQPDESYHGLTYAKAFG--------KMAYITKATAQLMRDLGSIQSPQ\n+NAFLLNLGLETLHLRMPQHCRNAQAVAEYLEKNERVAWVNYCGLKSNKYY\n+ELGQKYLPNGSCGVIAFGLKGTK----EDAIRFMDSLKMICIVTHVADAR\n+TCVLHPASHTHRQLSDEQLREAGVAPDLIRLSVGIENVEDIIEDIQQALD\n+ASK-------------\n+>693979.Bache_3197\n+--------------------------------------------------\n+----------MAKQFKPETLCVQAGWT--PKKGEPRVLPIYQSTTFKYET\n+SEQMARLFDLEESGYFYTRLQNPTNDAVASKIAALEGGVGAMLTSSGQAA\n+NFYAVFNICEAGGHLVCSSCIYGGTYNLFGVTMKKLGIDVTFVNPDAPEE\n+EIEAAFRPDTKALFGEVISNPTLEVLDIEKFARIAHSHGVPLIVDNTF-P\n+TPINCHPFEWGADIVTHSTTKYMDGHATSVGGAIVDSGNFDWEAHADKFP\n+GLCMPDESYHGLTYTKNFG--------KMAYITKATAQLMRDLGSIQSPQ\n+NAFLLNLGLETLHLRMPQHCKNAQAVAEYLSKNDKVAWVNYCGLPEDKYH\n+ELAQKYMPNGSCGVVTFGLKGGR----EVATKFMDSLKLAAIVTHVADAR\n+TCVLHPASHTHRQLSDEQLLAAGVRPDLIRFSVGIENADDIILDIEQALN\n+A---------------\n+>585543.HMPREF0969_02597\n+--------------------------------------------------\n+----------MAKQFKPETLCVQAGWT--PKKGEPRVLPIYQSTTFKYDT\n+SEQMARLFDLEDSGYFYTRLQNPTNDAVAAKIAALEGGVAAMLTSSGQAA\n+NFYAIFNICQAGDHFVCSSTIYGGTFNLFGVTLKKLGIDVTFVNPDASEK\n+EISAAFRPNTKALFGETISNPTLEVLDIEKFARIAHSHGVPLIVDNTF-P\n+TPINCRPFEWGADIVVHSTTKYMDGHATSVGGAIVDSGNFDWDAHADKFP\n+GLCTPDESYHGLTYTKAFG--------KMAYITKATAQLMRDLGSIQSPQ\n+NAFLLNLGLETLHLRMPQHCKNAQAVAEYLAQNDKVAWVNYCGLPGDKYY\n+EQAQKYMPNGSCGVVTFGLKGGR----EESIKFMDSLKLAAIVTHVADAR\n+TCVLHPASHTHRQLTDEQLMEAGVRPDLIRFSVGIENAEDIIADIEQALN\n+A---------------\n+>471870.BACINT_04892\n+--------------------------------------------------\n+----------MAKQLKPETLCVQAGWT--PKKGEPRVLPIYQSTTFKYET\n+SEQMARLFDLEENGYFYTRLQNPTNDAVAAKIAALEGGVAAMLTSSGQSA\n+NFYAIFNICQAGDHFVCSSTIYGGTFNLFGVTMKKLGIEVTFVNPDAPEE\n+EISAAFRPNTKALFGETISNPTLEVLDIEKFARIAHSHGVPLIVDNTF-P\n+TPINCRPFEWGADIVVHSTTKYMDGHATSVGGAIVDSGNFNWDAYADKFP\n+GLCTPDESYHGLTYTKAFG--------KMAYITKATAQLMRDLGSIQSPQ\n+NAFLLNIGLETLHLRMPQHCKNAQAVAEYLSKNDKVAWVNYCGLPGDKYH\n+ELAQKYMPNGSCGVVTFGLKGGR----EVAIKFMDSLKLAAIVTHVADAR\n+TCVLHPASHTHRQLSDEQLMEAGVRPDLIRFSVGIENADDIIADIEQALN\n+A---------------\n+>763034.HMPREF9446_01270\n+-------------------------------'..b'-QKANEFIDSLQLISHLANVGDTK\n+SLIIHPAATTHQQLSEEAQIGAGVYPGLLRISVGIEHIDDIKADLQQAFE\n+KIK-------------\n+>743722.Sph21_3381\n+-----------------------ML------NIHRFDVLYAHT-STLINK\n+RLNILKKNPMSTKNLKFDTLQVHAGQE-VDPATNARAVPIYQTTSYVFNN\n+SEHGANLFALKEFGNIYTRIMNPTTDVFEKRIAALEGGVAAVAVASGQAA\n+QFLALTNILESGENFVTGSNLYGGTYNQFKVSLKRLGIEARFAKNDEAA-\n+AIEALIDDKTKAIYIETIGNPSFNIPDFEAVAAVARKFELPLIVDNTFGA\n+GGYLFKPLEHGAHVVVESATKWIGGHGTSIGGVIVDGGNYDWGNG--KFK\n+QFSEPSEGYHGLVFKDVFGVNGPFG--NIQFAIRARVEGLRDFGPALSPF\n+NSFLLLQGLETLSLRVQRHVDNALSVAKWLEQHPLVQSVNYPGLESHPAH\n+ARAKKYLQHGFGAVLSFELKGEK----ESATAFVDSLQLISHLANVGDTK\n+TLIIQPSATTHQQLSDEEQLAAGVTPTALRLAVGIEHIDDIIADLQQAFE\n+KIK-------------\n+>391596.PBAL39_01047\n+--------------------------------------------------\n+--------MS--ANYKFETLQLHAGQE-IDPTTGSRAVPIYQTTSYGFKN\n+SEHGANLFALKEFGNIYTRIMNPTTDVFEKRIAALEGGVAALAVSSGQAA\n+QFIALNNILEAGDNFISSSHLYGGSYNQFKVAFKRLGIEVRFANGDDAD-\n+DFETKIDANTKAIYLESIGNPSFSIADFERLSAIANKHDLPLIVDNTFGA\n+AGYLFRPLDHGAHIVVQSATKWIGGHGTSIGGVIVDGGTYNWGNG--KFK\n+QFTDPSEGYNGLVFNDVFGIGGPFG--NIQFAIRARVEGLRDFGPALSPF\n+NSFLLIQGLETLSLRVQRHVDNALALATWLEQHAQVKLVNYPGLESSPYH\n+ANAKKYLQNGFGAVLSFELHGDK----SQATALVDHLKLISHLANVGDAK\n+TLIIQPSATTHQQLSETEQAAAGVTPNLLRISVGIEHIDDIKADLEQAFA\n+LIRK------------\n+>485917.Phep_1875\n+--------------------------------------------------\n+--------MS--ASHKFETLQVHAGQE-IDPTTGSRAVPIYQTTSYGFKN\n+SEHGANLFALKEFGNIYTRIMNPTTDVFEKRVAALEGGVAALAVASGQAA\n+QFIALNNILEAGDNFVSSSHLYGGSYNQFKVAFKRLGIEVKFANGDDPS-\n+DFEAKIDANTKALYVESIGNPAYSIIDFEKLAAIANKHDLPLIVDNTFGA\n+AGYLFKPLEHGAHIVVQSATKWIGGHGTSIGGVIVDGGNYNWGNG--KFK\n+QFTEPSEGYHGLVFNDVFGIGGPFG--NIQFIIRARVEGLRDFGPAIAPI\n+NSFLLLQGLETLSLRVQRHVDNTLALATWLENHEAVKSVSYPGLESSPYH\n+ANAKKYLQNGFGAVLSFELKGDK----EQATALVDSLKLVSHLANVGDAK\n+TLIIQPSATTHQQLSEDEQIAAGVKPNQLRVSVGIEHIDDIKADFEQAFA\n+SIKK------------\n+>762903.Pedsa_1156\n+--------------------------------------------------\n+--------MS-TQNLKFETLQVHAGQE-VDPTTGSRAVPIYQTTSYVFNS\n+NEHGANLFALKEFGNIYTRIMNPTTDVFEKRVAALEGGVAALATSSGQAA\n+QFLAITNILQAGDNFVTTGRLYGGTYNQFKVQFKRLGIEARFAKDDNPE-\n+SYEELIDENTKALYVETIGNPELNIPDFDGIAAVAKKHDIPFIVDNTFGA\n+GGYLFRPIEHGANIVVEAATKWIGGHGTSIGGVIVDAGNYNWGNG--KFP\n+QFSEPSEGYHGLVFSDVFGVNGPFG--NIQFIIRARVEGLRDYGCSQSPF\n+NSFLLIQGLETLSLRVQRHVDNTLELAKWLETHPKVKSVNYPGLESSPYH\n+ALAKKYLKNGFGGVLSFEVIGDK----ENATKVINALKLTSNLANVGDAK\n+TLIIQPSATTHQQLSEQEQIAAGVKPAALRVSVGIEHIDDIKADFEQALA\n+AI--------------\n+>714943.Mucpa_5529\n+--------------------------------------------------\n+--------MS--TQ-KFETLQLHAGQE-VDPTTGSRAVPLYQTTSYVFKN\n+AEHGANLFALKEFGNIYTRIMNPTTDVFEKRIAALEGGVAALATASGQAA\n+QFIALNNILQVGDNFVSSPFLYGGTYNQFKVAFKRLGVEARFAHDDSAE-\n+SFEALIDSNTKALYLETIGNPGFNIPDFEKIAALANKYDLPLIVDNTFGA\n+GGYLFRPLEHGAHVVVESATKWIGGHGTSIGGVIVDGGNYNWGNG--KYP\n+QFTEPSEGYHGLVFADVFGVGGPFG--NIQFIIRARVEGLRDFGSSQSPF\n+NSFLLIQGLETLSLRVQRHVDNALELAKWLENHPQVAKVNYPGLESSAHH\n+QLAKKYLKNGFGAVLSFEIKGEK----ENAGQFINSLQLVSHLANVGDAK\n+TLIIQPSATTHQQLSDTEQAAAGVTPTQLRVAVGIEHIDDIKADFEQAFA\n+KIKHLELEEA------\n+>504472.Slin_0217\n+--------------------------------------------------\n+--------M---SELHFDTLQLHAGQE-VDPTTNARAVPIYQTTSFVFND\n+SAHGADLFALKAFGNIYTRIMNPTSDVFEKRVAALEGGVAALAVASGQAA\n+QFIALSNILSAGDNFVTTSFLYGGTYNQFKVSFKRLGIEARFADGDKPE-\n+SFAKLIDENTKAIYLETIGNPGFNIPDFDAFAALAKEYDLPLIVDNTFGA\n+GGYLFRPLEHGAAVVVESATKWIGGHGTSIGGVIVDGGTYNWGNG--KFP\n+QFSEPSEGYHGMVFSDVFGVGGPFG--NIQFIIRARVEGLRDWGPAISPF\n+NSFLLLQGLETLSLRVDRTVQNALALAQWLEQHEQVEAVNYPGLESSPYH\n+ELAKKYLKRGFGGVFSFKVKGGN----EAANEFVNSLKLVSHLANVGDSK\n+TLIIHPAATTHQQLSEQEQASAGVEVGVLRVSAGIEHIDDIKADFEQAFA\n+RIAEPVIG--------\n+>269798.CHU_0274\n+--------------------------------------------------\n+--------M---S-FNFETLQLHAGQE-VDPTTQSRAVPIYQTTSYVFKD\n+SNHGANLFALKEFGNIYTRIMNPTTDVFEKRIAALEGGVAALATSSGQSA\n+QFIALTNILQAGDNFVTTSFLYGGTYNQFKVSFKRLGIEARFAEGDQVA-\n+SFEKLIDAKTKALYVETIGNPEFNIPDFEAFAALAKKHDLPLIVDNTFGA\n+GGYLFRPLEHGANVVVESATKWIGGHGTSVGGVIVDGGNYNWGNG--KFP\n+QFSEPSEGYHGLVFWDVFGTNGPFG--NIAFIIRARVEGLRDFGPSQSPF\n+NSFLLLQGLETLSLRVDRHVQNAQKLAEWLEQHADVATVNYPGLQSSKYH\n+NLAKKYLKRGFGGVLSFEIKGGK----SRAAQFINSLKLASHLANVGDAK\n+TLIIHPASTTHQQLSDEEQKVAGVSAGLLRVSVGIEHIDDIIADFEQAFE\n+TVKEIEHTVSVSEQV-\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.058.AA.strNOG.ENOG411BBR6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.058.AA.strNOG.ENOG411BBR6.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,341 @@\n+>88036.EFJ10116\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------MAPKLDPS--LHLKAFDDGGKLAEGLADHISK\n+LSAASIERKGAFTVVLSGGSLVSALTKLAQAPVVDQIDWSRWHVFWVDER\n+VVRKDDPDSSYKLAHDLFLSKVTIPVSQVYSINDALDAEAAADDYQALIA\n+HSIQTGILDTSQQ---GLPRFDLILLGMGPDGHIASLFPNHPLIQERQRW\n+VCSIADSPKPPPQRITMTLPVINAAANVVFVASGASKAEMVARVFGE-EL\n+PAGELPAQMILPHDGNLVWYVDRAAAGQHGC-------------------\n+---------\n+>88036.EFJ34542\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------MAPKLDPS--LHLKAFDDGGKLAEGLADHISK\n+LSAASIERKGAFTVVLSGGSLVSALTKLAQAPVVDQIDWSRWHVFWVDER\n+AVRKDDPDSSYKLAHDLFLSKVTIPVSQVYSINDALDADAAADDYQALIA\n+HSIQTGILDTSQQ---GLPRFDLILLGMGPDGHIASLFPNHPLIQERQRW\n+VCSITDSPKPPPQRITMTLPVINAAANVVFVASGASKAEMVARVFGE-EL\n+PAGELPAQMILPLDGNLVWYVDRAAAGQYGR-------------------\n+---------\n+>3218.PP1S1_158V6.1\n+MAAPM-IRA-----C-C---SA--------ANARPTLPFCS---P-----\n+TPPLRPSN---------------LLSHSGISVNSRRSSVSVVR-----RG\n+-----VGWR---G---VLRGVA--------------V--SGL--------\n+GSWAL-SGVG-RRTVSMASSLGKLKR--EELQVYDDAEQLNASLAAHVAD\n+VAKAAIEARGLFSVVLSGGSLIKSLGKLCESPYLESIDWARWHVFWADER\n+VVKKDHPDSNYKLAWDGLLSKVPIPPGQLYAINDALSTEAAAEDYETCIK\n+QLTKTGVVGTAD----GYPRFDLLLLGMGPDGHCCSLFPHHPLVQVKDKW\n+IAPITDSPKPPPERITFTMPVVQAAANITFVANGEGKAEMLAKIFGE-EL\n+PLGDLPSQSARPLNGKLIWFVDKPAASKL---------------------\n+---------\n+>4513.MLOC_38507.2\n+MSTSMTVSV-----S-A-A-AS--------SSLPPLSARRR---S-----\n+PPASLVPV---------------R------S----L---RSSP---R--P\n+-----RLLS---S---ARTTP---------------VL-LPA--------\n+A---A-MATD-G--AAA--APAGSSK--RDLLIFDAEENLAVSLAKYTAD\n+LSAKFAAERGAFTVVLSGGSLIHALRKLTEAPYLETVDWTKWHVFWVDER\n+VVPKDHEDSNYKLALDGFLSKVPIPTGQVYAINDALSAEGAAEDYETILK\n+QLVKNGVLAMSKT--TGFPRFDLQLLGMGPDGHIASLFPGHPLVKENKKW\n+VTHILDSPKPPPQRITFTFPVINSSAYVAMVVTGAGKAGAVQKAISDK-K\n+TSDLLPVEMAVLDDGEFTWFTDKEAVSMLQN-------------------\n+---------\n+>15368.BRADI4G35867.1\n+MS--V--SV-----S-A---AA--------FSSHPPLSRRR---S-----\n+PPASRLPP---------------N------SHRIQL---HSGPKPRR--P\n+-----RLLS---S-----ARA---------------PI-LPT--------\n+A---A-MATD-S--AAPA-ASGAGSK--RNLLIFDAEEDLAVSLAKYTAD\n+LSAKFAAERGAFTVVLSGGSLIEALRNLAEPPYLETVDWSKWHVFWVDER\n+VVPKDHEDSNYKLALDGLLAKVPIPPGQVYAINDALSAEGAADDYETVLK\n+QLVKNGVLAMSTA--TGFPRFDVMLLGMGPDGHIASLFPGHPLVKENQKW\n+VTHIKDSPKPPPERITFTFPVINSSAYVAMVVTGAGKAGAVQKALSDKQA\n+SSDLLPVEMAILQDGEFTWFTDKEAVSMLQNK------------------\n+---------\n+>4577.GRMZM2G148769_P01\n+MSTSV--SA---------A-AV--------AALVPPLTGRR---S-----\n+PPASRVPQ---------------I------CRR------RIRS---K--P\n+-----RIFS-------SSPSF---------------PI-VPA--------\n+A---A-MATG-G--AAPT-ASDAGSK--KKLLILDSEEDLAVSLAKYTAE\n+LSEKFAAERGAFTAVLSGGSLIEALRKLTEPPYLDSVDWSKWHVFWVDER\n+VVPKDHVDSNYKLAYDGFLSKVPIPPGQVYAINDALSAEGAADDYEACLK\n+QLVKNGVISMSAA--TGFPRFDLQLLGMGPDGHIASLFPGHPLVNEKERW\n+VTYIKDSPKPPPERITFTFPVINSSAYVAMVVTGAGKAAAVQKALSDKQT\n+SSDLLPVEMAVLQDGEFTWFTDKAAVSLLQNK------------------\n+---------\n+>4558.Sb02g030620.1\n+MYTSV--SAAAVAAA---A-AA--------AALVPRLTGRR---S-----\n+APASRIPE---------------I------CRR------RIRS---K--P\n+-----RTFS-------SSPSF---------------PI-VPA--------\n+A---A-MATD-G--AA----SDAGSK--KKLLIFDSEEDLAVSLAKYTAE\n+LSEKFAAERGAFTAVLSGGSLIQALRKLTEPPYLDSVDWSKWHVFWVDER\n+VVRKDHVDSNYKLAFDGFLSKVPIPPGQVYAINDALSAEGAADDYEACLK\n+QLVKNGVISMSAA--TGFPRFDLQLLGMGPDGHIASLFPGHPLVNEKERW\n+VTYIKDSPKPPPERITFTFPVINSSAYVAMVVTGVGKAGAVQKALSDKQT\n+SSDLLPVEMAVLQDGEFTWFSDKPAVSMLQNN------------------\n+---------\n+>4555.Si030554m\n+MSTSV--SA---------A-AA--------AALLPTLTGRR---S-----\n+PPASRVPA---------------I------FCR------RIGP---R--P\n+-----RLFS---S---CSLPF---------------PI-RPA--------\n+A---A-MATD-G--AAP-------AK--QKLLIFDTKEDLAVSLAKYTAD\n+LSKKFAAERGAFTVVLSGGSLIDALSKLTEPPYLESVDWSKWHVFWVDER\n+VVPKDHEDSNYKLAFDGFLSKVPIPPGQVYAINDALSAEGAADDYEACLK\n+QLVKNGVIAMSAA--TGFPRFDLQLLGMGPDGHIASLFPGHPLVNEKERW\n+VTYIKDSPKPPPERITFTFPVINSSAYIAMVVTGAGKAGPVQKALSDKQT\n+SSDLLPVEMAVLQDGEFTWFTDKPAVSMLQNK------------------'..b'047627\n+M--AE---C-----A---L-SL--------ASSSPVLS------R-----\n+ISPTRFSP---------------I------RRPILLTSSFVAG---K--P\n+-----LFCS---H---PHRRNS--------------VL--ST--------\n+NSWRS-RCR-TK--ASMAERV----R--AKVEVYDSEEELAVALAKYTAD\n+LSEKFCKERDAFTVVVSGGSLIKSLRKLVEPPYIDSIDWSKWHVFWVDER\n+VVPKDHPDSNYLLAYDGFLSKIPIPAGHVYAINDALSAEAAADDYETCLR\n+HLVKSKILDISKE--SGFPKFDVMLLGMGPDGHIASLFPGHPLVHEKEKW\n+VTFIKDSPKPPPNRITFTFPVINSSANIALAIVGAGKADVVHKSLGD-DK\n+SSDLLPVQMVSP-EGELVWFLDKDAASKL---------------------\n+---------\n+>4081.Solyc07g066270.2.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------MAETVSGESK--AEVKVYDSDEELAVALAKYTAD\n+LSEKFCKERDVFTVVVSGGSLIKSLRKLVEPPYIDSIDWSKWHVFWVDER\n+VVPKDHPDSNYLLAYDGFLSKIPIPAGNVHAINDALSAEAAADDYETCLR\n+HLVKSKILDISEE--SGFPKFDVMLLGMGPDGHVASLFPGHPLVHEKAKW\n+VTFIKDSPKPPPNRITFTFPVINSSANIALAIVGAGKADVVHKSLGD-DK\n+SSDLLPVQMVSP-EGELVWFLDKDAASKL---------------------\n+---------\n+>3694.POPTR_0015s00970.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------MADQNNK--KVVKVYDTEQDVAVSLAKYVAD\n+LSAKFAKERGSFTVVLSGGYLIDSIRKLTEPPYVDSVEWSKWHVFWVDER\n+VVPRNHVDSNYKLAFDGFLSKVPIPAGQVYAINDALSAEGAAEDYQTVLK\n+HLVDTGVLAKSSV--TGFPKFDLMLLGMGPDGHVASLFPGHPLLEENVKW\n+VTHIMDSPKPPPQRITFTFPVINSSAYIAMVVCGPGEVDAVYKALGK-TE\n+NPELLPVQRVTP-EEELRWFLDKVAASKLQE-------------------\n+---------\n+>3694.POPTR_0012s03150.1\n+MATAA---S-----S---L-TF--------STSLPKLCRPL---S-----\n+ISITQLP------------------------------QVSLNF---K--K\n+-----LNCS---I---SSALKI--------------SR--RT--------\n+AATTT-KASSMA--SSGITTVDQKNK--KVVEVFDTEEELAVSLAKYTAD\n+LSDKFAKERGSFTVVVSGGSLIKSLRKLVEAPYVDSIDWSKWHVFWVDER\n+VVPKDHPDSNYKLAFDGFLSKVPIPPGNVYAINDALSAEGAADDYETCLK\n+HLVHTGVINKSSV--SGFPKFDLMLVGMGPDGHVASLFPGHPLLKENQKW\n+VTHITDSPKPPPGRITFTFPVINSSSYIALVVCGAGKASVVQTALGK-SQ\n+NSDVFPVQMVSP-EGELKWFLDRDAASKL---------------------\n+---------\n+>3694.POPTR_0015s00960.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------MA--SSGITTIDQNNK--KVVEVFDTEEDLAVSLAKYTAD\n+LSDKFAKERGAFTVVVSGGSLIKSLRKLVEAPYVDSIDWSKWQVFWVDER\n+VVPKDHPDSNYKLAFDGFLSKVPIPPGNVYAINDALSSEGAADDYETCLK\n+HLVHTGVINISSL--SGFPKFDLMLVGMGPDGHVASLFPGHPLLKENQKW\n+VTHITDSPKPPPERITFTFPVINSSAYIALVVCGAGKASIVQTALGK-SQ\n+NSEVFPVQMVSP-EGELKWFLDKDAASKL---------------------\n+---------\n+>88036.EFJ25522\n+--------------------------------------------------\n+----------------------MQ------KKK-----------------\n+----------------------------------------EE--------\n+KDDEK-IDQS-PR--HLFQYPDGPSQ--ATFFRFDDVEEVSSALAEYIVQ\n+VSNEAIKQRGKFTFVLSGGSIVKALRFLAEGPVFHSIAWDKWNVFWVDER\n+VVPLNHEDSNYKLAKDEFLSKVPIPHEQIHAIQNFHDEKAAAHAYESKLR\n+ELVRKKVIATKTT--KKFPRFDFVLLGLGPDGHVASLFPNRPSLAEEKLW\n+VLPISNSPKPPSKRITMTLPCINAAEHVAFVALGSGKAHVLHRVLER-PA\n+LPGSLPAQMVRVDDGNLVWFADQGATSELHLENWNNAKQFPFFDFKQPAS\n+VSS------\n+>88036.EFJ22231\n+--------------------------------------------------\n+----------------------MQ------KKK-----------------\n+----------------------------------------EE--------\n+KDDEK-IDHS-PR--HLFQYPDGPSQ--ATFFRFDDVEEVSSALAEYIVQ\n+VSNEAIKQRGKFTFVLSGGSIVKALRFLAEGPVFHSIAWDKWHVFWVDER\n+VVPLNHEDSNYKLAKDEFLSKVPIPHEQIHAIQNFHDEKAAAHAYESKLR\n+ELVRKKVITTKTA--KKFPRFDFVLLGLGPDGHVASLFPNRPSLAEEKLW\n+VLPISNSPKPPSKRITMTLPCINAAEHVAFVALGSGKAHVLHRVLER-PA\n+LPGSLPAQMVRVDDGNLVWFADQGATSELHLENWNNAKQFPFFDFKQPAS\n+VSS------\n+>3218.PP1S260_17V6.1\n+MAFSF--SAY----A---A-PGAVSTPRLVESVAQGNGTQSALPSRLSYG\n+QNIVKFPGFVCAASVNEVGEGSSN------AAP----------------P\n+RRGRPKSTNSSTTTKAVRKNAEGKRVVDGTASDEYAHM-KET--------\n+ENQNG-KPKP-AV--HLFEYEDGPWP--CSVSIVPHLHDVAEAVADYIAR\n+ISEESIKARGYFSIVLSGGSLVKALSALVKEPHASKLNWSKWFVFWADER\n+MVPISHADSNYNDAKHEFLSKVPIPDDNLVTIDDWDVCSAAANGYEARLK\n+EMVKRKILHTTNVNHHKFPRFDLVLLGIGPDGHVASLFPNSLQLAETKKW\n+VVPITKSPKPPSRRISLSLPCINGAAHVAIVVVGSSKAEVLQRVFER-PA\n+LPGALPAQLVRPRHGELAWFVDKQAAGRLSIEHYNDPKKFPFLDWSSLKE\n+AKESTGNQI\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.059.AA.strNOG.ENOG411BBRR.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.059.AA.strNOG.ENOG411BBRR.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,378 @@\n+>4641.GSMUA_Achr1P18250_001\n+M------------A-CS-FPVLDLEKLRGEER-----------EQSMDLL\n+RDACEKWGFFELLNHGISHELM-DEVERRTKAHYEQCRKQKFKQL-ACKA\n+LKSGPG-T-----DVTDMDWESTFFLRHLPVSNMSDFPDMDEEY-----R\n+KAMTEFATGLEKLAERLLDLLCENLGLEEGYLKNAFYG-SK-G-PNFGTK\n+VSNYPPCPRPELIHGLRAHTDAGGIILLFQDDRVSGLQLLKDGQWIDVPP\n+MHHSIVVNLGDQIEVITNGKYKSVLHRVVARSDG-NRMSIASFYNPSGDA\n+VIYPAPSLVQK-----EA-E------AYPRFVFEDYMKLYVTQKFQAKQP\n+RFEAMKATVT---VNGQPTPTP\n+>4538.ORGLA02G0295500.1\n+MAGGLTSPPIRRSSPRWSLESDNVDQIDTARRSRQMWIEAAFVGPPLRTG\n+RGGRRRATTAQMLNHGIAHELM-DEVERVSKAHYANCREEKFKEF-ARRT\n+LEAGEK-----GADVKGIDWESTFFVRHRPVSNLADLPDVDDHYSYCNQR\n+QVMKQFASEIEKLSERVLDLLCENLGLEKGYLKKAFAGS--NG-PTFGTK\n+VSSYPPCPRPDLVDGLRAHTDAGGIILLFQDDQVSGLQLLKDGEWVDVPP\n+MRHAIVANIGDQLEVITNGRYKSVMHRVLTRPDG-NRMSIASFYNPGADA\n+VIFPAPALAAAEA----ERA-DAAAAAYPRFVFEDYMNLYVRHKFEAKEP\n+RFEAMKSAAEVV--HAAPIATA\n+>39947.LOC_Os02g53180.1\n+MAGGLTSPPIRRSSPRWSLESDNVDQIDTTRRLRQMWIEAAFVGPPLRTG\n+RGGRRRAATAQMLNHGIAHELM-DEVERVSKAHYANCREEKFKEF-ARRM\n+LEAGEK-----GADVKGIDWESTFFVRHRPVSNLADLPDVDDHY-----R\n+QVMKQFASEIEKLSERVLDLLCENLGLEKGYLKKAFAGS--NG-PTFGTK\n+VSSYPPCPRPDLVDGLRAHTDAGGIILLFQDDQVSGLQLLKDGEWVDVPP\n+MRHAIVANIGDQLEVITNGRYKSVMHRVLTRPDG-NRMSIASFYNPGADA\n+VIFPAPALAAA----------DAAAAAYPRFVFEDYMNLYVRHKFEAKEP\n+RFEAMKSAAEVV--HAAPIATA\n+>15368.BRADI3G57620.1\n+-------MAASDADAPLSFPVISMEKLETEER-----------GAAMEVI\n+RDACENWGFFELLNHGISHELM-DEVERVTKAHYAECREHKFQEF-AART\n+LEAGEK-----GADVKDVDWESTFFVRHLPASNLADLPDLDDHY-----R\n+RVMKEFATEIEKLAERLLDILCENLGLEQGYLKKAFAGS--GGLPTFGTK\n+VSSYPPCPRPDLVDGLRAHTDAGGVILLFQDDQVSGLQLLKDGRWVDVPP\n+MRHAVVVNVGDQLEVITNGRYKSVMHRVRTRADG-NRMSIASFYNPGADA\n+VIFPAKELVAGKE---KKEG-VKEEEVYPRFVFEDYMDLYVRHKFEAKEP\n+RFQAMKSSAAVV--VDAPIATA\n+>4513.MLOC_54272.1\n+MA-----IPANAAATSLSFPVIHMEKLETEER-----------GAAMEVI\n+RDACENWGFFELLNHGISHELM-DEVERVSKAHYAACREEQFKEF-AART\n+LEAGEK-----GADVKDVDWESTFFVRHLPASNLADLPNLDHHY-----R\n+QVMKEFASEIEKLAEKVLDLLCENLGLEEGYLKRAFTGS--NG-PTFGTK\n+VSSYPPCPRPDLVDGLRAHTDAGGVILLFQDDQVSGLQLLKDGAWVDVPP\n+MRHAVVVNIGDQLEVITNGRYKSVMHRVLTRPDG-NRMSVASFYNPGADA\n+VIFPAPALMGAAEAAGKNEG-EEGTAEYPSFVFEDYMNLYLRHKFEAKEP\n+RFEAMKVDA-------APIATV\n+>4513.MLOC_58642.1\n+MA-----IPANAAAASLSFPVINMENLETEER-----------GAAMEVI\n+RDACENWGFFELLNHGISHELM-DEVERVSKAHYAACREEQFKEF-AART\n+LEAGEQ-----GADVKDVDWESTFFVRHLPASNLADLPDLDHHY-----R\n+QLMKQFASEIEKLAEKVLDLLCQNLGLEQGYLKRAFDGS--KG-PTFGTK\n+VSSYPPCPRPDLVDGLRAHTDAGGVILLFQDDQVSGLQLLKDGAWVDVPP\n+MRHAVVVNIGDQLEVITNGRYKSVMHRVLTRPDG-NRMSIASFYNPGADA\n+VIFPAPALVAAAGAAERNEG-EEGTAVYPRFVFEDYMDLYLRHKFEAKEP\n+RFKAMKADA-------APIATA\n+>4533.OB02G40990.1\n+------------MATGASFPVINMEKLETEER-----------GAAMEII\n+RDACENWGFFEMLNHGISHELM-DEVERVTKAHYANCREEKFKEF-ARRT\n+LEAGEK-----GADVKDVDWESTFFVRHLPVSNLVDLPDVDDHY-----R\n+QVMKEFASEIEKLSERVLDLLCENLGLEKGYLKKAFAGS--NG-PTFGTK\n+VSSYPPCPRPDLVDGLRAHTDAGGIILLFQDDQVSGLQLLKDGGWVDVPP\n+MRHAIVANIGDQLEVITNGRYKSVMHRVLTRPDG-NRMSIASFYNPGADA\n+VIFPAPALVAGA-----EEE-RADAASYPRFVFEDYMNLYVRHKFEAKEP\n+RFEAMKSSAEVV--HAAPIATA\n+>4555.Si017837m\n+---------MAATGTTLSFPVINMEKLQTKEK-----------PATMAVL\n+NDACENWGFFELLNHGISHELM-DEVERLNKAHYTSCREPKFQEF-AART\n+LEAGEK-----GADVKDVDWESTFFVRHLPASNLADLPDLDDHY-----R\n+QVMKQFASEIQKLSEKLLDLLCENLGLEKGYLKQAFAGS--NG-PTFGTK\n+VSAYPPCPRPDLVDGLRAHTDAGGIILLFQDDQVSGLQLLKDGEWVDVPP\n+MRYAIVVNIGDQLEVITNGRYKSVTHRVLTRPDG-NRMSIASFYNPGADA\n+VIFPAPALVAA----------EEERAAYPRFVFEDYMNLYVRQKFEAKEP\n+RFEAMKSA----------IATA\n+>4577.GRMZM2G052422_P01\n+-----------MAATVSSFPVVNMEKLETEER-----------ATAMEVI\n+RDGCENWGFFELLNHGISHELM-DEVERLTKAHYATFREAKFQEF-AART\n+LEAGEK-----GADVKDVDWESTFFVRHLPASNLADLPDVDDRY-----R\n+QVMEQFASEIRKLSERLLDLLCENLGLEPGYLKAAFAGS--DG-PTFGTK\n+VSAYPPCPRPDLVDGLRAHTDAGGIVLLFQDDQVSGLQLLRGGEWVDVPP\n+MRHAIVANVGDQLEVITNGRYKSVMHRVLTRPDG-NRMSVASFYNPGADA\n+VIFPAPALVGAA-----E-E-DRAEAAYPSFVFEDYMNLYVRHKFEAKEP\n+RFEAMKSA----------IATA\n+>4558.Sb04g034520.1\n+-----------M-AATASFPVVNMEKLETEEK-----------ATAMEII\n+RDACENWGFFELLNHGISHELM-DEVERLTKAHYANFREAKFQEF-AART\n+LEAGDK-----GADVKDVDWESTFFVRHLPASNLADLPDVDDHY-----R\n+QVMKQFASEIQKLSEKLLDLLCENLGLEPGYLKSAFAGS--NG-PTFGTK\n+VSAYPPCPRPDLVDGLRAHTDAGGIILLFQDDQVSGLQLLKDGEWVDVPP\n+MRH'..b'---EIDDLDWESTFFLRHLPESNLAEIPDLGEDY-----R\n+KTMKEFALELEGLAEQLLDLLCENLGLEKGYLRKVFCG-SK-G-PTFGTK\n+VSNYPPCPKPDLIKGLRAHTDAGGIILLFQDDKVSGLQLLKDGQWIDVPP\n+MKHSIVINLGDQLEVITNGKYKSVLHRVLAQTDGT-RMSIASFYNPGSDA\n+VIYPAPELVEK-----EE-K---ESQIYPKFVFEDYMKLYAGLKFQAKEP\n+RFEAMKAVESTI--NMGPIATA\n+>3847.GLYMA02G43560.1\n+M------------T--N-FPLINLEKLSGEER-----------NDTMEKI\n+KDACENWGFFELVNHGIPHDIL-DTVERLTKEHYRKCMEERFKELVASKG\n+LDAVQ--T-----EVKDMDWESTFHLRHLPESNISEIPDLIDEY-----R\n+KVMKDFALRLEKLAEQLLDLLCENLGLEKGYLKKAFYG-SR-G-PTFGTK\n+VANYPPCPNPELVKGLRPHTDAGGIILLFQDDKVSGLQLLKDGQWVDVPP\n+MRHSIVVNIGDQLEVITNGKYKSVEHRVIAQTDG-TRMSIASFYNPGSDA\n+VIYPAPELLEK-----EA-E-E-KNQLYPKFVFEDYMKLYAKLKFQAKEP\n+RFEAFKA----S--NFGPIATV\n+>3847.GLYMA14G05390.1\n+M------------T--N-FPVINLEKLNGEER-----------NDTMEKI\n+KDACENWGFFELVNHGIPHDLL-DTVERLTKEHYRKCMEERFKEFMASKG\n+LDAVQ--T-----EVKDMDWESTFHLRHLPESNISEIPDLIDEY-----R\n+KVMKDFALRLEKLAEQLLDLLCENLGLEKGYLKKAFYG-SR-G-PTFGTK\n+VANYPPCPNPDLVKGLRPHTDAGGIVLLFQDDKVSGLQLLKDGQWVDVPP\n+MRHSIVVNIGDQLEVITNGKYRSVEHRVIAQTDG-TRMSIASFYNPGSDA\n+VIYPAPELLEK-----EA-E-E-KSQLYPKFVFEDYMKLYAKLKFQAKEP\n+RFEAFKA----S--NFGPIATA\n+>4081.Solyc12g005940.1.1\n+M------------E--N-FPIINLEKLNGAER-----------VATMEKI\n+NDACENWGFFELVNHGIPHEVM-DTVEKLTKGHYKKCMEQRFKELVAKKG\n+LEGVE--V-----EVTDMDWESTFFLRHLPSSNISQLPDLDDVY-----R\n+EVMRDFAKRLEKLAEELLDLLCENLGLEKSYLKNTFYG-SK-G-PNFGTK\n+VSNYPPCPKPDLIKGLRAHTDAGGIILLFQDDKVSGLQLLKDGRWIDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVMHRVIAQKDG-TRMSLASFYNPGNDA\n+LIYPAPALVDK-----EA-E-EHNKQVYPKFMFDDYMKLYANLKFQAKEP\n+RFEAMKAMESD------PIAIA\n+>4113.PGSC0003DMT400036081\n+M------------E--N-FPIINLEKLNGAER-----------AATMEKI\n+NDACENWGFFELVNHGIPHEVM-DTVEKLTKGHYKKCMEQRFKELVAKKG\n+LEGVE--V-----EVTDMDWESTFFLRHLPSSNISEIPDLDDVY-----R\n+EVMRDFAKRLEKLAEELLDLLCENLGLEKSYLKNTFYG-SK-G-PNFGTK\n+VSNYPPCPKPDLIKGLRAHTDAGGIILLFQDDKVSGLQLLKDGQWIDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVMHRVIAQKDG-TRMSLASFYNPGNDA\n+LIYPAPALVDK-----ET-E-AHNKQVYPKFVFDDYMTLYANLKFQAKEP\n+RFEAMKAMESD------PIEIA\n+>4081.Solyc07g049550.2.1\n+M------------E--N-FPIINLENLNGDER-----------AKTMEMI\n+KDACENWGFFELVNHGIPHEVM-DTVEKLTKGHYKKCMEQRFKELVASKG\n+LEAVQ--A-----EVTDLDWESTFFLRHLPTSNISQVPDLDEEY-----R\n+EVMRDFAKRLEKLAEELLDLLCENLGLEKGYLKNAFYG-SK-G-PNFGTK\n+VSNYPPCPKPDLIKGLRAHTDAGGIILLFQDDKVSGLQLLKDEQWIDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVMHRVIAQTDG-TRMSLASFYNPGNDA\n+VIYPAPSLIE------------ESKQVYPKFVFDDYMKLYAGLKFQPKEP\n+RFEAMKAMEANVE-LVDQIASA\n+>4081.Solyc07g049530.2.1\n+M------------E--N-FPIINLEKLNGDER-----------ANTMEMI\n+KDACENWGFFELVNHGIPHEVM-DTVEKMTKGHYKKCMEQRFKELVASKG\n+LEAVQ--A-----EVTDLDWESTFFLRHLPTSNISQVPDLDEEY-----R\n+EVMRDFAKRLEKLAEELLDLLCENLGLEKGYLKNAFYG-SK-G-PNFGTK\n+VSNYPPCPKPDLIKGLRAHTDAGGIILLFQDDKVSGLQLLKDEQWIDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVLHRVIAQTDG-TRMSLASFYNPGSDA\n+VIYPAKTLVEK-----EA-E--ESTQVYPKFVFDDYMKLYAGLKFQAKEP\n+RFEAMKAMESD------PIASA\n+>29760.VIT_12s0059g01380.t01\n+M------------E--A-FPVINMEMLNGEER-----------GATMEMI\n+KDACENWGFFELVNHGISHEQM-DAVEKLTKGHYRKCMEQRFKELVAAKA\n+LEGVQ--T-----EIKDMDWESTFFLRHLPVSNVSDFPDLDEEY-----R\n+KVMKDFALKLEKLAEELLDLLCENLGLEKGYLKKAFHG-SK-G-PNFGTK\n+VSNYPPCPKPDLIKGLRAHTDAGGIILLFQDDTVSGLQLLKDGQWVDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVLHRVVAQTDG-NRMSIASFYNPGNDA\n+VIYPAPALLEK-----EA-E---KDQVYPKFVFDDYMKLYAGLKFQAKEP\n+RFEAMKNVEASV--NMGPIATA\n+>3694.POPTR_0002s21750.1\n+M---------------E-FPVINMEKLNGEER-----------AATMEKI\n+RDACENWGFFELLNHGIAHEFL-DTVERMAKEHYKKGMEQRFKELVASKA\n+LVGVQ--T-----EIKDMDWESTFHLRHLPMSNIAEIPDLDDEY-----R\n+KVMKEFALKLEKLAEELLDLLCENLGLEKGYLKRAFCG-SS-GSPNFGTK\n+VSNYPPCPKPDLVKGLRAHTDAGGIILLFQDDKVSGLQLLKDGQWIDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVEHRVIAQTDG-TRMSIASFYNPGNDA\n+VIYPAPALVEK-----EA-E-E-KKHLYPKFVFDDYMKLYAGLKFQAKEP\n+RFEAMKAVETNV----------\n+>3694.POPTR_0014s15710.1\n+M---------------E-FPVISMEKLNGEER-----------AATMEKI\n+KDACENWGFFELLNHGISHEFL-DTVERMTKEHYKKCMEQRFKELVASKA\n+LDGVQ--T-----EIKDLDWESTFQLRHLPKSNIAEIPDLDDEY-----R\n+KVMKEFALKLEKLAEELLDLLCENLGLEKGYLKRAFYG-SN-GSPTFGTK\n+VSNYPPCPKPDLVKGLRAHTDAGGIILLFQDDKVSGLQLLKDGQWIDVPP\n+MRHSIVVNLGDQLEVITNGKYKSVEHRVIAQTDG-TRMSVASFYNPGSEA\n+VIYPAPALVEK-----EA-E-E-KKNVYPKFVFDDYMKLYAGLKFQAKEP\n+RFEAMKAVETTV--NLGPIATA\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.060.AA.strNOG.ENOG411BBWK.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.060.AA.strNOG.ENOG411BBWK.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1190 @@\n+>3711.Bra029329.1-P\n+----------------------------------MVMDKRAEAEYTRAKT\n+SVWWDIENCAVPRGCDAHGITKKLSAALANMNYCGPLSISSYGNTDLIPK\n+AVQLALSSTGISLNHVPS-GRKDASDKKILVDMFLWVVENPPPANIMLIS\n+GDIDFSDALHRLRMRRYNILLAHPQ--NISPSLVASAKTSWLWRSLLLAS\n+GSSLTQCGSSGVLDGSE-------ITSEDVSEHVLSTQAMDSGSGSSKAA\n+RSKLKGIYV-PKAPNELLVKEAN-----RKKLQK------KC-----SET\n+K--------------------------------------N-----V----\n+----------------------E--ES-------VQNND-----------\n+-------QESLKCLEKQNKELMETITT-SERN-----------------V\n+APLNVDY-VYGELSRDFPVPK-----------------------------\n+--------EVRESFDAIPMKLEPTQNEIVIEELEGMLKQILQIKSGEPET\n+APAGLSENLKEDMNKKK-KKRNKKKSRVIEED------------------\n+---------------KAEPYVCSICSVICDSPAIFESHLNGRKHAAMVEK\n+HAEALLGDKQIPYDVVQHNGHLIDGEASE---------------------\n+-----------NIDYFEDVPEID---------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------Y----KPLPNE\n+EA--REWIDAIFNTQELSQNANLTLEFESM-----------LNQ------\n+---SLEMNSGDYEGVTEHPEEFKDKVSKD-KA-ESEAYVC-----SICSV\n+VCAC-PTV------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----FESHLMGRRHA-----------------------------------\n+--------------------------------------------------\n+-------------------------AKVLFD-----DKKILEESLKEKDH\n+PRDSMVKILEVSLEDT--------SK-QTVVEAGS---------------\n+-----------------TSERVEEEKHAATVKKRE--PV--VKKHDAVVK\n+KQAG------------------TKFAY-----------------------\n+---VRKNGP-----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------------\n+>3711.Bra012979.1-P\n+------------------------------MCFDSSITHTAEAEYATAKT\n+SVWWDIENCPVPKGWDAHSIAKKLNSALVNLNYRGPLTISAYGNTDLIPK\n+AVQQALSSAGISLNHVPS-GKKDASDKKILVDMFLWVLENPAPANLMLIS\n+GDGDFSYALNRLRMLRYNILLAHPL--QASPFLVASARTSWMWRSLIASG\n+CHSSRSCCSFGSEM--S-------SQDASVSEHALSTQAMDFGSGSSKAA\n+RKKLKDVL------KELNQQETN-----RMKLQK------KC-----SET\n+G--------------------------------------E-----S----\n+----------------------E--L------------------------\n+--------LCNVACKSIEVFTTGKEPA-AQAL-----------------V\n+DAKDSDL-KSQDAQESEKSGR-EFWQDFKERLDKNGVAPLNVDHVFSE-L\n+SRDFHVPKEVRECFEAIFKKLEPTQNDIEIEKLESMLKQGLEIESNEPGK\n+APAEPTENLEGDMTKKK-S--------TVIEDKYEP-YVCTICNVVCAHP\n+SVFE-SHH-KGRKHVAKFKLHIDAM-LDNKHIQEEVIQ-----DN-----\n+--------------G---LPKDMTKELQIKPVKAPEN-I-----------\n+----DDQ-RQEL------REGCDE--------------EN-FQ-T-----\n+--------------------------------------------------\n+---------------------------------------------IEE--\n+V-----------------------------CENDYKSLPN----AECIFT\n+EL--N------------------------PEFPASEES---RECIDAIFK\n+--KPEVSQDANLTRELESIPSQNLE-----------MNSGDSEGSSAGG-\n+TEHP-EEY------------MDMKKEK-----------------------\n+-------VA-----------------------------------------\n+----------------------KDK------KAELKAYVCSICSV--ICL\n+SPTVFEAHLMGRKHAKGVKKH-----------------------------\n+--------------------------------------------------\n+-------------------------AEVLFD-----DKKILEQSLEENVH\n+SRDAA------EELQIESKDAQVSIKEVTQISKAR-VDNKDSEQILSVEF\n+AEPKEAS----------RERFDSIVK-RLDLFMEKTSKQ----TLV---E\n+SEKA------------------SEGKKHAATL------------------\n+-RKHVPLVKKEV--------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------AVV------\n+>3847.GLYMA1280S00200.1\n+MGGH------------------------------------AATTYSAAKI\n+SVWWDIDNCRVPKGHNANSIAQNITSALVGINYAGPLSISAYGDTNRIPP\n+PVQHALSSTGVSLNHIPT-GANDASDMKILVDMLLWAVDNPAPANYLLIS\n+GDTNFSNALHQLSLRKYNILLAHPPH--VSPSLAAAAKVVWLWTTLSA-G\n+GPPLSDSTSN----------SCKPPTP------APLLQPFQFKPK-----\n+---PKY---------------IR---KITTITPI-------------ETK\n+--------------------------------------NNDAEPLP----\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------'..b'GKD\n+SKGFCA--GK----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----GPELSLNKKNPEGENSKGSGEGKGPEL-EHDPQKKPRSRNRKKPRS\n+RNKKKPE---GEDSKGSGEGKGPELKHDPQKEPGSSNKMKPGGENSKGSC\n+EGEGPELKHDPQKKPEGENKKKQEGENSRGSCEGKGPELKHDPHKKPEGE\n+NKKKQEGENSGGSCEGKGPELKHDPDKKPEGENKKVARARKGVSLKKS--\n+VLTRSKRRVSLTKLDKGKKNP--------------LCCESRRGMTAS\n+>3694.POPTR_0005s00580.1\n+M-------------------GGER---G--G-----GGGRAEAQYVTAKI\n+SVWWDIENCHVPRDCDPHAIAQNISSALVKMNYCGPVSISAYGDTHRINS\n+AVQQALSSTGIALNHVPA-GVKDASDKKILVDMLFWAVDNAAPANYLLIS\n+GDRDFSNALHQLRMRRYNILLAQPQK--ASAPLLAAAKSVWLWTSLLA-G\n+GPPLSEGESLQPDSNSYM--STSDTSQIPLTDAAQLKQPADSYSENSYLA\n+NQKSPYT--ARGYDNKQKGKNIR---RSPSQTNG------SK-------T\n+T--------------------------------------S-----VPL--\n+-WTQED--------------QHN--TN-------SHQPG-----------\n+----T--------------------------------------YFPRVPL\n+SGPAPDF-VHGNTNFTWCDVPYVNG-------NHQNHYTQQLRPNN-S-A\n+--------------------------------------------------\n+---------------------------------MQP----------DFAA\n+GGFY-P-P-Y--LHP------------------------------RG---\n+------------------------------------PPP-----------\n+----MP-ARP---------NGTSS-MPAPYMSAPDIGNLNI----SGYSI\n+NF--NP--------QRRNPEVKHDSKKKLPRSVSS----SNSQNGNMAHN\n+SPSI--YQDEMPNHRYSSHPEYLSSS-----SSA-MGASVAPGSVIWG-S\n+PGCP-KPSEY-VQGLIGVVLL-------ALNTLKSEKIMPTETN------\n+---IAD------------------------CIRHG----DQ-----KQR-\n+--------NTDIKKALECAIEHQMVVAQ-SLG-AMQLFVGKNEK------\n+LWKCV-NPIGGSPKQIPKAT------------------------------\n+----WDEIQL----FLISPAGRSAILASQCRYEAGTI-------------\n+LKRKCLKGHALGDILQILNMVIGYKKWIIHHPSGWQPISITLSEI--ESD\n+LWSAEG--T-----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------------\n+>3694.POPTR_0013s00450.1\n+M-------------------GGGR---GGGG-----GGGGAEAQYMTAKI\n+SVWWDIENCHVPMGCDPHAIAQNISSALVKMNYCGPVSISAYGDTHRIDS\n+AVQQALSSTGIALNHVPA-GVKDASDKKILVDMLFWAVDNPAPGNYLLIS\n+GDRDFSNALHQLRMRRYNILLAQPQK--TSASLLAAAKSVWLWTSLLA-G\n+GPPLTEGELQKLCSNNYM--STSDTKQIPVSDAAQIKESVDSYSEKPYVA\n+NQKSPYT--PRGHDNKQKGKNIQ---RNPSQINT------SK-------T\n+T--------------------------------------S-----SPL--\n+-WTQED--------------HHN--SN-------SHQPG-----------\n+----P--------------------------------------SFPKVPP\n+SGPGLDF-VPGNNNFTWSDNTHING-------NYQNHYTQQLRPNN-P-G\n+--------------------------------------------------\n+---------------------------------MRP----------EFAA\n+GGLY-P-P-HPNLHP------------------------------RA---\n+------------------------------------PPP-----------\n+----MP-VRP---------NGTSF-TSAPYTSAPDIGILNI----PGHPV\n+NF--NP--------QRRNPELKHDPKKKLPRSVSL----SNSQNGNMAHN\n+SPSV--YRDEKPNHRYPGGPEYPPSS-----SHA-MGASVAPGSDKWG-S\n+QGCP-KPSEY-VQGLIGVVLL-------ALNTLKSERIMPTETN------\n+---IAD------------------------CIRYG----DL-----KHR-\n+--------NTDIKKALESAIKHQMVATR-SLG-AMQLYVGKNEK------\n+LWKCV-NPVGGKAKQIQKAT------------------------------\n+----WNEIHQ----FLRSSAGRSAILASECRYEAGTI-------------\n+LKSKCLKEHVLGDVLQILNMVIGYKKWIIPHQSGWRPLSITIAEKA-NSD\n+SGSTEG--TF----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----GSTEGTFGWDTGSTEGTFGWDTGSTEG-TFGGDSGTTEGTFGCEWG\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1023 @@\n+>4555.Si019932m\n+--------------------------------------------------\n+-------------MEKTMQPLWSSCNNRRSKTMHVPLLGVAL--VLLL--\n+-F-----LASPPTSCKEEEKTSLLGFLDGLS--Q-NSGLTTSWQN-ATNC\n+CLWEGIICNVDGAVMDISLTSRGLEGHIS-PSLGNLTSLLRLNLTGNSLS\n+GGLPLELLLSSSIAVLDVSFNKLNGEFHELQST--RDSMMKVINISSNLF\n+TGNFPS-TTIGSMKNLAALNMSNNCFTGEIPSTLCVDKPYFVVLDLSYNQ\n+FHGRIPTELGNCSGLRVLRAGKNQLIGTLPAELFNVTSLEHLSFPKNH-L\n+QGTLE--HVGKLRNLVILDLGWNGLNGKIPDSIGQLKKLEELHLDNNNMS\n+GELPSALRNCSNLTTIILKDNNFQGELKRVNFSTLSNLRFLDCRSNKFTS\n+TIPASLYSCSNLIALRLSFNNLHGQFSLGISNLRSLRFLALSHNNFTNIT\n+NALQILGKSRTLALLLIGGNFKHETMPDYDTFYGFENLMCLAINECSLYG\n+HLPNWLAKLKNLRGLLLDNNKLSGPIPTWIDRLNLLFYLDISNNNLTGDM\n+PTALMEMPTLQS----AHSDP-IV--LKFPIYLTPFL--QYRTTSGFPKM\n+LNLGNNKLTGMIPPQIGQLQALLTLNLSFNNLHGEIPQSIGNLTNLQVLD\n+LSYNDLTGAIPSSLEMLHFLSKFNISSNDLEGSVPTGDQFSTFPDSSF--\n+--------------------------------------------------\n+---------------------------------------------HLSGG\n+L-------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------\n+>4577.GRMZM2G410963_P01\n+--------------------------------------------------\n+-----------------MQPLQYSYNNRKSEMLHIPLLGVSL--VLLL--\n+-F-----LASPASSCKEEEKTSLFEFLNGLS--Q-ASGLTSSWQN-DTNC\n+CLWEGVICNGDRTIIDISLAAMGLEGHIS-PSLGNLNGLLKLNLSGNLLS\n+GGLPSTLLLSSSITVLDVSFNKLSGEFHELQST--PNSAMKVMNISSNFL\n+TGYFPS-TTLEGMKNLAALNMSNNSFAGEIPSTICVDKPFFVVLDLSYNQ\n+FVGRIPSELGNCSGLKVLKAGQNQLNGTLPSEIFNVTSLEHLSFPNNH-L\n+QGTLDPECIGKLRNLVILDLGWNGLNGKIPNSIGQLKRLEELHLDNNNMS\n+GELPPALSSCSNLTTIILKDNNFQGDLNHVNFSTLSNLKFLDCRSNKFTG\n+TIPESLYSCSNLIALRLSFNNLHGQFSSGINNLKSLRFLALAHNSFTNIR\n+NTLQILSKSRTLTLVLIGGNFKHETMPDDDEFHGFENLMGLGINKCPLYG\n+KLPNWLAKLKNLRALLLDDNKLSGPIPAWINSLNLLFYLDISNNNLTGDI\n+PTALMEMPTLEA----AHSAP-II--LKFPVYLAPFL--QYRTTSGFPKM\n+LNLGNNKFNGIIPPEIGQLQALLTLNLSFNNLHGEIPQSVGNLTNLQVLD\n+LSYNNLTGEIPSVLERLHFLSKFNISSNDLEGPVPTGGQFSTFPDSSF--\n+---------------FGNPKLCGATLMRHC-NSADAVPVTDVSTEE----\n+---------------------------YADKVIFAVA-----FGMFFGVG\n+VLYDQM-------------FLFRYIYFG----------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------\n+>4558.Sb04g003870.1\n+--------------------------------------------------\n+-----------------MQPLQYSCNNRKSEMLHIPLLGVAL--VLFL--\n+-S-----LASPAISCKEEEKTSLFEFLNGLS--Q-ASGLTSSWQN-DTNC\n+CLWEGVICNVDGTVIDISLAAMGLEGHIS-PSLGNLNGLLKLNLSGNLLS\n+GELPPKLLLSRSLTVLDVSFNKLSGEFHELQST--PDSAMKVMNISSNFL\n+TGYFPS-TTLEGMKNLAALNMSNNSFAGEIPSTVCVDKPFFVVLDLSYNQ\n+FIGRIPPELGNCSGLRVLKAGQNQLNGTLPAEIFNVTSLEHLSFPNNH-L\n+QGTLDPERVGKLRNLAILDLGWNGLNGKIPNSIGQLKRLEELHLDNNNMS\n+GELPPALSSCSNLTTIILKDNNFQGDLKRVNFSTLSNLKFLDCRSNKFTG\n+TIPESLYSCSNLIALRLSFNNLHGQFSSGINNLKSLRFLALAHNNFTNIT\n+NTLQILSKSRSLALVLIGGNFKHETMPDYDEFHGFENLMCLAINECPLYG\n+KLPNWLAKLKNLRGLLLDNNKLSGPIPAWINSLNLLFYLDISNNNLTGDI\n+PTALMEMPTLEA----AHSDP-II--LKFPIYLTPF'..b'V----\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-GLIDLKYSHYSKAYSVAPQSPAPSKMNTPKENLIGQLVICQRDSVNAVY\n+APKSRKLGRN----\n+>4533.OB02G13590.1\n+--------------------------------------------------\n+-----------------MNPIPHSWRS----SICINFFGPAI--MLLL--\n+-I-----FISPVSSCAEQESHSLLQFLAGLS--Q-DGGLAASWQN-STGC\n+CTWEGIICSAEGAVSEILLASRGLEGKIS-PSLGELTGLSRLNLSHNSLS\n+GVLPAQLMSSGSITVLDVSFNRLNGHLPELNSSV-SDQPLQVLNISSNRL\n+TGEFSS-TIWEKMRSLVAINASNNSFTGYIPFSFCISSPSLAMLDVSYNQ\n+FSGNIPPGIGKCTGLRMLKAGHNNISGTLPDDLFQVKSLEYLSFPKNG-L\n+QGTINGALMIKLSNLVFLDLGGNRFSGKIPDSIGQLKKLKELHMDHNNID\n+GELPSSLGNCTNLEIIILTNNRLMGELAKVNFSNLPNLKNLDICMNYFTG\n+KIPASIYSCSNLTWLRLSFNKLHGQLTEKIGNLKSLTYISISYNNFTNIT\n+GALHILKSLSNLTTLLIGGNFMHEAMPEDETIDGFENLQGLGMNDCALTG\n+KVPSWLSKLKKLKLVLLYNNQLSGPIPTWINNLKSLMYIDISNNSLTGEI\n+PLALMEMPMLKSDKIGDDSD-LRA--FLMPVYVDPSL--QYRTAIAFPRM\n+LNLGNNKLSGAIPMEIGQLKALLSLNLSFNNLNGEIPQSISNLRNLMRLD\n+LSSNHLTGEIPSALANLHFLSKFNISYNDLEGIVPIGGQFSTFPSSSF--\n+---------------AGNPKLCNPMLLHHC-NSAEQAPASPISTKQ----\n+---------------------------YIDKVVFAIA-----FGVFFGIG\n+VLYDQI-------------IIFR--YFG----------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------\n+>39946.BGIOSGA008306-PA\n+--------------------------------------------------\n+----------------------------------MNFFHLAL--VLLL--\n+-L---SFICAPVGSCIEQERLTLLRFLAELSPPHDNGQLAASWRN-RTDC\n+CTWEGIICDVDGAVTEILLASRGLEGRIS-SSLSELTSLSRLNLSYNSLS\n+GGLPPELIFSGSIVVLDVSFNRLGGELQEVDSSS-SDWPLQVLNISSNLF\n+TGAFPS-TTWEKMSNLVAINASNNSFTGHIPSSFCISSLSFAALDLCYNQ\n+FSGEIPAGIGKCSALRMLKAGHNNISGALPDDLFHATSLEYLSFPNNG-L\n+QGTIK--LVIKLSNLVFLDLGGNSFSGKVPESIGELKKLEELRMDHNYIS\n+GELPSTLANCTNLAAIVLVSNKFTGDLAKVNFSNLPNLKTLDLCTNYFTG\n+TIPASIYSCSNLTWLRLSFNKLHGQLPEETEKLKSLTFVSLSYNYFTNIT\n+GALHILKSLRNLTTLLIGGNFMHETIPQDETIHGLENLQVLGINDCALTG\n+KIPSWLSKLKKLELLLLYNNQLSGPIPTWIKSLNYLKYVDLSNNSLTGEI\n+PTSLTEMPMLRSDKIADHSD-PRL--FRMPVFVAPSL--EYHTANAFPKM\n+LNLGNNKFSGVIPMEIGQLKALLSLNLSFNNLHGEIPQSASNLKNLMVLD\n+LSSNHLTGAIPSSLANLHFLSNFNISYNDLEGPVPITGQFSTFPTSSF--\n+---------------AGNPKLCSPMLLHRC-NSAGAAPVSTIPTKQ----\n+---------------------------YIDKVVFAIA-----FGMFFGVG\n+VLYDQI-------------VVSR--FFG----------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.062.AA.strNOG.ENOG411BCX3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.062.AA.strNOG.ENOG411BCX3.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,22869 @@\n+>4538.ORGLA10G0113900.1\n+------------------MSRVVLPLLI-LVAA-----------------\n+-----------------AAAIPAP-ANAATPT-EAEALLAWKASLQDDAA\n+ALSGWSRAA------------------PVC--R-WHGVACD-S-----GR\n+VAKLRLR---------------------------------GAGLSG---G\n+LDKLDFAALPALIELDLNGNNLTG-----------AI-------------\n+PASVSRLSSLASLDLGNNGFTDSIPPQLGD--LSDLVDLRLY--------\n+-----------------------------------------NNNLVGAIP\n+HQLSRLPNIVHFDLGANYLTDQ--E-FAKFSPMPTVTFMSLYLNSFNGSF\n+PDFILKSPNVTYLDLSQNTLFG--------------------------QM\n+P-DTLPEKLPNLRYLNLSINSFSGLIPASLGRLTKLQDLRMAGNNLTGGI\n+PEF-LGSMPQLRILELGDNQLGGAIPPVLGRLHMLQRLDIKNAGLVSSLP\n+SQLGNL----KNLTFLELSLNQLTGGLPPAFAGMKAITDFGIATNNLTGE\n+IPPVLFTSWPELISFQVQNNSLTGKIPPELGKAKKLQF------------\n+------------LYLFTNNLTGSIPAELGELENLTELDLSVNSLTG----\n+--------------------------------------------------\n+------------------------------------------------P-\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------IPSSLGK\n+LKQ-----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------LTKLELF--FN-NL------------------\n+--------------------------------------------------\n+-------TGVIPPE-IGN--MTALQSLDVNTNS---L-------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---HGELPA--------------------------------T-ITDL---\n+--------------------------------------------------\n+-RSLQYLAVFDNH-----------------------MSGTIPA-------\n+--------------------------------------------------\n+DLG-------KGL------ALQHVSFTNN-SFS---GEL----PRHIC--\n+DGFA-L--DHLTAN----YNNF------------------SGTL-----P\n+PC-LK---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------NCTALVRVRLEENHFTGDISEAFG\n+VHPKLAYLDVSGSKLAGELSSDWGQCTNLTYLSINGNSISGNLDSTFCTL\n+SS------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------LQFLDL\n+SNNRFNGELPSCWWELQALLFMDISGNGFSGELP--ASKG----------\n+-------------------L--QLPLQSMHLANNSFSGVFPNII-R-KCG\n+-ALVTLDMGNNKFFGHIPSWIGTSLPLLRILILRSNNFSGEIPTELSQLS\n+QLQLLDMASNVLTGFIPTSFGNLSSMT-QTKT-LPV--TEYFNA-E-STP\n+FQPEV---PQVPKPHRR-RE-PK-N------Q--SPLDQSR------DRV\n+SIQWKGHEETFQRT----A-M--LMTGIDLSGNSL---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------YGEIPKELTYLRGLRF---LNL\n+SRNDLSGSIPERIGNLNILESLDLSC-NELSGIIPATISNLSSLSVLNLS\n+NNHLQGRIPTGSQLQTLVDPSIYSNNLALCGFPLSIACHASMAIFLLAAL\n+S'..b'-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------SANSFH-GPI-----------P---\n+-------TSI-GNL------------------------SSLR-----YLS\n+LSGN------------------------PLINGT----------------\n+---------------------------------LPM-SL----WFLSNLE\n+N------------------------LNVGGTSL-TGTISEV---HFTAL-\n+S--------KLK----------------------VLSI---SG----T-S\n+L-SFHVNSSW----------------------TPPFQ-------------\n+------------LEYLDADSCK------------------------MG--\n+---------------------PKFPAWLQ-TQKSLFYLDFSRSGIVDTAP\n+N-W-----------------------------------FWKFASY-----\n+------------------I------QQIHLSNNQISG---DLSQVVLNN-\n+----------------T--------IIDLSSNCFSGRLPRL---SPN--V\n+-------------------------VVLNIANNSFSGQ-----IS-----\n+------------------------------PFMCQKMN-GR-SKLEVVDI\n+SINVLSGEL--------------------------SDCWMHWPSLTHVSL\n+GSNNLSGKIPNS-----MG-S-LVGLEALSLENNSFYGEIPSS-LEN-CK\n+-VLGLINLSDNKFSGIIPRWIFE-RTTLIIIHLRSNKFMGKIPPQICQLS\n+SLIVLDLADNSLSGSIPKCLNNISAMT---AG-PIRG---IW--Y-----\n+--------------DA-----LE-A--DYDY------------ESYMESL\n+VLDIKGREAEYEKI----L---KYVRMIDLSSNNL---------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------SGSIPIEISSLVGLQF---LNL\n+SRNHLMGRIPKKIGVMASLESLDLSR-NHLSGEIPQSMSNLTFLDDLDLS\n+FNNFSG--------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------RIPSSTQLQSFD\n+P---LS------FFGNPELCGAP-------LTKNCTKDEE-TL-GP---T\n+A------------V---EE----NREFP--EISWFYIGMGSGFIVGFWGV\n+CGAL----------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--FFKR-------AWRYAYFQ-FL--------------------------\n+--------------------------------YDI-RD-RA-YV------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------------A---------\n+--------------IPIK---LKW-FHQ-KLRR-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------Y-H----------AG----KEK------IYDYPYFQIIY\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.063.AA.strNOG.ENOG411BDBU.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.063.AA.strNOG.ENOG411BDBU.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,420 @@\n+>4513.MLOC_45161.2\n+-------------M-----RV-----KLELLMPLMAQYKTPA-WATLIAG\n+FFVLLALS----LSMYLIFEHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESYVSLINPNINVYCGILREGYEALAMYC\n+FGRYITACLGGEEKTIAFLKREGGSDSGQPLLHH--AS-DKGIIHHHFPV\n+NFILKPWRMGTQFYQIIKFGIFQYVIIKTLTASLSLFLEAFGVYCEGEFN\n+LRCGYPYFAAILNFSQFWALYCLVEWYTATKDELAHIKPLAKFLSFKSIV\n+FLTWWQGVVIAIMYSLGLLRSPLAQSLELKSSIQDFIICIEMGIASAVHL\n+YVFPAKPYEHFVNQSPGNISVLGDYASSD-PIDPEEVKESNRPSKMKLPQ\n+FEPDERSATNIKESVRDFVVGSGEYVIKDFNFTVNQALRPVEKRFD----\n+------KLMKKKDKY-KNTQDDNWVSAASP-ER-P-VRGIDDPLLSGSAS\n+D-SGVLKGKKH-RRVVNTVAAADSWGGG----DKTPDGYEIRGRRWAVKN\n+>15368.BRADI5G18390.1\n+-------------M-----RV-----NLELLMPLMAQYTAPT-WATLVAG\n+FFVLLALS----LSMYLIFEHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESYVSLIDPNTNVYCGILRDGYEAFAMYC\n+FGRYITACLGGEDKTIAFLKREGGSGSGQPLLHD--AP-EKAIIHHHFPV\n+NLILKPWRMGTRFYQIIKFGIFQYVIIKTLTASLSLFLEAFGVYCEGEFN\n+LRCGYPYFAAVLNFSQFWALYCLVEWYTATKDELAHIKPLAKFLSFKSIV\n+FLTWWQGVVIAIMYALGMLRSPLAQSLELKSSIQDFIICIEMGIASVVHL\n+YVFPAKPYELLANQSPGNISVLGDYVSSE-PVDPYEIRESNRPSKMKLPQ\n+FEPDERSATNIKESVRDFVIGSGEYVIKDFKFTVNQAVRPVEKRFD----\n+------KLMKKKDKY-KKSQDDNWVSAKSP-ER-P-VRGIDDPLLSGSTS\n+D-SGVMKGKKH-RRDFSSVAAVDSWGGG----DKTPDGYEIRGRRWAVKS\n+>4533.OB04G28730.1\n+-------------M-----RV-----NLKLLMPLLTQYTTPT-WATLVAG\n+FFVLLSLS----LSTYLIVDHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESYVSLINPNTTVYCGILRDGYEAFAMYC\n+FGRYITACLGGEDKTIAFLKREGGSGAGQPLLDH--TS-EKGIIHHHFPV\n+NFILKPWRLGMRFYLIIKFGIFQYVIIKTVTASLSLFLEAFGVYCDGEFN\n+LRCGYPYFAAVLNFSQYWALYCLVEWYTATKDELAHIKPLAKFLSFKSIV\n+FLTWWQGVVIAIMYSLGLLRSPLAQSLELKSSIQDFIICIEMGIASIVHL\n+YVFPAKPYELRANQTPGNISVLGDYVSSD-PVDPFEVKESSRPTKLKLPQ\n+LEPDERSSTNIKQSVRDFVVGSGEYVIKDFKFTVNQAVRPVEKRFD----\n+------KLMKKND---KKSQDDNWVNAASP-DR-P-VRGIDDPLLGGSAS\n+D-SGVTKGKKH-RRAVSTVAVVDSWGGG----DLASDGYEIRGRRWAVKN\n+>4538.ORGLA04G0187600.1\n+-------------M-----KV-----NLRLLMPLLAQYTTPT-WATLVAG\n+FFVLLSLS----LSIYLIFEHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESYVSLINPNTSVYCGILRDGYEAFAMYC\n+FGRYITACLGGEDKTIAFLKREGGSGSRQPLLDH--AS-EKGIIHHHFPV\n+NFILKPWRLGMRFYLIIKFGIFQYVIIKTVTASLSLFLEAFGVYCDGEFN\n+LRCGYPYFAAVLNFSQYWALYCLVEWYTATKDELAHIKPLAKFLSFKSIV\n+FLTWWQGVVIAIMYSLGLLRSPLAQSLELKSSIQDFIICIEMGIASIVHL\n+YVFPAKPYELQANQSPGNVSVLGDYVSSD-PVDPFEIKESNRPAKLKLPQ\n+LEPDERSTTNIKESVRDFVVGSGEYVIKDFKFTVNQAVRPVEKRFD----\n+------KLMKKN----KKSQDDNWVSAVSP-DR-P-VRGIDDPLLGGSTS\n+D-SGFTKGKKH-RRAVSTVAAADSWGGG----DLASDGYEIRGRRWAVKN\n+>4555.Si010013m\n+-------------M-----RV-----NIGLIVPVMAQYSAPT-WATIVAG\n+LFTLVALS----LSMYLIFEHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESYISLINPNTSVYCGILRDGYEAFAMYC\n+FGRYITACLGGEDKTIAFLKREGGSGSGQPLLHH--AS-EKGIIHHHFPV\n+NFILKPWRLGTRFYLIIKFGIFQYMIIKTLTASLSLLLEPFGVYCEGEFN\n+LRCGYPYFAAVLNFSQYWALYCLVAWYTATKDELAPIKPLAKFLSFKSIV\n+FLTWWQGVVIAILYALGLLRSPLAQSLELKSSIQNFIICIEMGIASAVHL\n+YVFPAKPYALLANQSPGNISVLGDYVSSD-PVDPFEIKESNRPTKMKLPQ\n+LEPDERSVTNIKESVRDFVVGSGEYVIKDFKFTVNQAVRPVEKRFD----\n+------KLMKKKDKH-KKTQDDNWVSAATP-ER-P-IRGIDDPLLSGSAS\n+D-SGVTKGKKH-HRVVSSNAAMDSWGGG----DQASDGYEIRGRRWAVKN\n+>4558.Sb06g025370.1\n+-------------M-----RV-----NIGLLVPLMAQYSTPM-WATLVAG\n+FFMLLALS----LSMYLIFEHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESYISLINPNTSVYCGILRDGYEALAMYC\n+FGRYITACLGGEDKTIAFLKREGGSGSGQPLLHH--AS-EKGIIHHHFPV\n+NFVLKPWRLGTRFYLIIKFGIFQYVIIKTLTATLSLLLEPFGVYCDGEFN\n+LRCGYPYFAAVLNFSQYWALYCLVAWYTATKDELAPIKPLAKFLSFKSIV\n+FLTWWQGVVIAIMYALGLLRSPLAQSLELKSSIQDFIICIEMGIASVVHL\n+YVFPAKPYALLTNQSPGNISVLGDYVSSD-PVDPFEIKESNRPTKMKLPQ\n+FEPDERSVTNIKESVRDFVVGSGEYVIKDFKFTVNQAVRPVEKRFD----\n+------KLMKKNDKR-KKSQDDNWVSAATP-ER-P-VRGIDDPLLSGSSS\n+D-SGVTKGKKH-RRIVSTAAAVDSWGGG----DQASDGYEIRGRRWAVKS\n+>4577.GRMZM2G082181_P01\n+-------------M-----RL-----NVGLLVPLMAQYSAPT-WATLVAG\n+FFMLLALS----LSTYLIFEHLSAYN------------------------\n+-NPEEQKFVLGVILMVPCYAIESCISLINPSTSVYCGILRDGYEAFAMYC\n+FGRYITACLGGEDKTIAFLKREGGSGSGQSLLHH--TS-EKGIIHHHFPV\n+NYVLKPWRLGTRFYLIIKFGIFQYVIIKTLTATLSLLLESFGVYCDGEFN\n+LRCGYPYFAAVLNFSQYWALYCLVAWYTATKDELAPIKPLAKFLSFKSIV\n+FLTWWQGVVIAIMYALGLLRSPLAQSLELKSSIQDFIICIEMGIASVVHL\n+YVFPAKPYALLTNQSHGNISVLGDYVSSE-PVD'..b'SISVDCAILRDCYEAFAMYC\n+FGRYLVACLGGEERTIEFMERQGRASSKTPLLEN--NC-EKGTVKHPFPM\n+NYFLKPWKLGQWFYQVIKIGIVQYMIIKSLSAILAVILEAFSLYCEGDFK\n+WGCGYPYIAVVLNFSQSWALYCLVQFYTVTKDELEHIKPLAKFLTFKSIV\n+FLTWWQGVAIALLYDLGLFKSAIAQGLQSKSSVQDFIICIEMGIASIVHL\n+YVFPAKPYELMGDRLSGSVSVLGDYASTD-PLDPDEVRDSERPTKLRLPH\n+PDIDIRSGMTIGESVRDVFIGGGGYIVNDVKFTVNQAVEPVEKGITKFNQ\n+KLHKISQNIKRHDKEKRKTKDDSCIT---PTRR-V-IRGIDDPLLNGSFS\n+D-SGVSRGKKH-R-RKSGYTSGESGGESSS--DQSYSAYQIRGGRWVTKD\n+>3694.POPTR_0004s21460.1\n+-------------------------------------FSTPL-WSTLISG\n+AFVLISLS----LSFYLLFEHLSAYK------------------------\n+-NPEEQKFLIGVILMVPFYAVESFVSLLDPSISVDIEILRDCYESFAMYC\n+FGRYLVACLGGEERTIEFLKREGRSSSKAPLLEH--SH-ERGTIKHPFPM\n+NYILKPWRLGQWFYQVVKFGIVQYMLIKSLTAVLAVILEAFGVYCEGDFK\n+LKCGYPYIAVILNFSQSWALYCLVQFYTATKDELAHIKPLYKFLTFKSIV\n+FLTWWQGVAIALLCSLGLFKSSIAQGLQFKSSLQDFIICIEMGIASIVHL\n+YVFPAKPYELMGDRFPGSVSVLGDYASVDCPIDPDEVRDSERPTKLRLPQ\n+PDIDVRSGMTIKESVQDVVVGGGGFIVNDVKFTVNQAVEPVEKGIIKFNE\n+KLHKISQDMKKH-KERRRTKDDSCIATASPARR-V-IRGIDDPLLNGSIS\n+D-TGVARGKKHHR-GTSGHTSGESGGESSS--DQS---YLIRGRRWVTKD\n+>3694.POPTR_0009s16710.1\n+MLYDISHLREKQAM-----KY-----LQDLIVYYLLTFSIPL-WDTLIAG\n+AFVLVSLS----SSFYLLFEHLSAYR------------------------\n+-NPEEQKFLIGVILMVPCYAVESFVSLLDPSISVDIEILRDCYESFAMYC\n+FGRYLVACLGGEERTIEFLEREGRSSSKAPLLEH--NH-ERGIIKHPFPM\n+NYIFKPWKLGQWFYQVVKFGIVQYMLIKSLTAVLAVLLEAFGVYCEGDFK\n+LRCGYPYMAVVLNFSQSWALYCLVQFYTAIKDELAHIKPLYKFLTFKSIV\n+FLTWWQGVAIALLYSLGLFKSPIAQGLQFKSSIQDFIICIEMGIASIVHL\n+YVFPAKPYELMGDRFPGSVAVLGDYVSVDCPVDPDEVRDSERPTKLRLPQ\n+PDIDVRSGMTIKESVRDVVVGGGGFIVNDVKFTVNQAVEPVEKGIIKFNE\n+KLHRISQNMKQHNKDKRRTKDDSCIATPSPTRR-V-IRGIDDPLLIGSFS\n+D-TGVARGKKHNR-RKSGYISGESGGESSS--DQSYGAYQVRGRRWVTKD\n+>88036.EFJ28171\n+M---LSWGLLLDRL-----DVGGSFILAAAPGPDDAVTSIHT-WAVIVAG\n+IFVLIALT----LSTFLIFEHLTSYN------------------------\n+-KPEEQKWLVGIIFMVPVYSVESLVSLWNNELSLVCDILRNCYEAFALYS\n+FGCYLIACLGGEDRVVDMLERQAIAGPRTPLLVRSRSS-GKAAVKHPIPL\n+NCCLTPWSLGQDFYHIVKFGIVQYMILKTTLSFLSLFLNVFDAYGEGEFK\n+WYYGYPYVTVILNFSQTWALYCLVQFYAVTKDELHHIQPLSKFICFKAIV\n+FATWWQGVAIAVLFGSGAAKGVAPEGVKLQSSLQDFIICIEMAIAAVAHI\n+YCFPARPYQQINEFGQRSVAVLSDYASMDSPLDPDEVKESERRSILRFLP\n+PEME-NVATSLKESVQDVVMVGGEQIVHDVKFTVSQAVEPMEKGINRLNE\n+TLHD-----KFHHKRLHASKDDAWIRQ--GLGG-A-VRGIDDPLLSGSVS\n+D-TGLLRKKFK---DSASYGSGAESSGESS--DQGGAGFKTGGRRWTLRS\n+>88036.EFJ29661\n+M---LSWGLLLDRL-----DVGGSFILAAAPGPDDAVTSIHT-WAVIVAG\n+IFVLIALT----LSTFLIFEHLTSYN------------------------\n+-KPEEQKWLVGIIFMVPVYSVESLVSLWNNELSLVCDILRNCYEAFALYS\n+FGCYLIACLGGEDRVVDMLERQAIAGPRTPLLVRSRSS-GKAAVKHPIPL\n+NCCLTPWSLGQDFYHIVKFGIVQYMILKTTLSFLSLFLNVFDAYGEGEFK\n+WYYGYPYVTVILNFSQTWALYCLVQFYAVTKDELHHIQPLSKFICFKAIV\n+FATWWQGVAIAVLFGSGAAKGVAPEGVKLQSSLQDFIICIEMAIAAVAHI\n+YCFPARPYQQINEFGQRSVAVLSDYASMDSPLDPDEVKESERRSILRFLP\n+PEME-NVATSLKESMQDVVMVGGEQIVHDVKFTVSQAVEPMEKGINRLNE\n+TLHD-----KFHHKRLHASKDDAWIRQ--GLGG-A-VRGIDDPLLSGSVS\n+D-TGLLRKKFK---DSASYGSGAESSGESS--DQGGAGFKTGGRRWTLRS\n+>3218.PP1S450_10V6.1\n+M----------NLH-----EAR-AAV--V---AIGSEASIHG-WAVLIAG\n+VFVLFSLS----LSSFLLFDHLSAYN------------------------\n+-DPEEQKWIIGIIFMVPVYGITAFISLWKPSLSLQSSILGNMYEAYALYS\n+FGCYLIACLGGEDTVIRKLDRQGLMGPSTPLLEH--SAGIRALVQHPAPL\n+KWCMDPWELGRPFYNAAKFGIVQYMILKTACALVALLLDLVNLYGDGEFT\n+WYNGYPYITVVLNFSQTWALYCLVQFYYVTHEELRDIKPLSKFVCFKSIV\n+FATWWQGVLLAFIFSLPLANS----WGNIQTSLQDFIICIEMAVAAVAHL\n+YIFPATPYHDLEGGKDRSVKVLADYAAFDSPLDPEEVRESERPSMVKFFG\n+VDVE-KGGTSVKESVHDVLVVGGNHVVHDMKVTMSQAVEPVEKGFTRINE\n+TIQFWGG--KLEEKKVRVTKDDTWVASQTTSYSED-VRGYDDPLLTGSVS\n+D-SGFWRARR------SNYGSAESSGGENS--DSGFGGFKTSGKRWTIRR\n+>3218.PP1S13_235V6.1\n+M----------KLY-----GVG-AAV--V---ALGLEGSAHD-WAILVAG\n+VFVLFSLS----LSTFLLFEHLSTYN------------------------\n+-DPEEQKWIIGIIFMVPVYGVTSFISLCKPDLSLRFSIVGNCYEAYALYS\n+FGCYLIACLGGEDTVVRKLDRQGLMGPRTPLLEH--SAGIRALVQHPAPL\n+KWCMDPWELGRPFYNAAKFGIVQYMILKTACALIALMLDFVNRYGDGEFT\n+WHNGYPYITVVLNFSQTWALYCLVQFYYVTHEELRDIKPLSKFVCFKAIV\n+FATWWQGVLLACIFSFPFVTS----SGNIQTSLQNFLICIEMAVAAIAHL\n+YVFPATPYHELEGGKDRSVKVLADYAAFDSPLDPEEVRESERPSMVKFFG\n+VDLE-KGATSVKESFHDVLVVGGNHVVHDMKVTMSQAVEPVEKGFTRINE\n+TIQFWGG--KQKEKKKKVSKDDSWVASQKTTHSDD-ARGYDDPLLTGSVS\n+D-SGFWRAKR------SSYGSADSSGGENS--DSGFGGFKTSGKRWTIKR\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.064.AA.strNOG.ENOG411BDKC.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.064.AA.strNOG.ENOG411BDKC.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,4914 @@\n+>4533.OB09G25500.1\n+--------------------------------------------------\n+----------------------------MSLTNFSNLVLSDSDGRVRWTT\n+NITGSAAGAGSAAVLLDTGNLVIDHRTAPTCGRASSTRPTRSSLGWISRT\n+RKVWTPGPWTGYTVWSQYHANTSDLIYFSIANNGKQRCITFSVSEGSPHT\n+SPNDTFDYFSHGTRGRKGIPRIWQTRQLLDEVLLCIHVALLCVQENPDDR\n+PVMSSFVCTLENGITALPAPSCPGYFAQRSSEIEL-FKDRTFLLSLKKVL\n+FKDGKKALKDRESFRSNKKYFELLVSRAVLMDLSAAFTYIVIGVI-----\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------------LLLPPPCAPDD\n+RLVAGKPLSPGV-TVVSDGGAFALGFFSPSNSTPEKMYLG--IWYNDV-P\n+R-RTVVWVAN--RETPVTKGTSSAPTM-SLTNSSNLVLSDADGRVRWTTN\n+VTGADSPT-AAGRPAAVLLST-GNLVIRSP-NGTT--LWQSFEHPTDSFL\n+-PGMKLAVA-YR-TRVSDRLVSW--RGPDDPSPGS--FSYGG-DPDTLLQ\n+-VFLWNGTRPVT--RDGPWTG-----------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+YM--VSSQYQANT--SDIIYFSV--VDVDEKRY--ITFSVSE--GSPHTR\n+--TFDACAGECSRNCS-CV--AYAYANLSSSRS-KGDMTRCL--VWSGEL\n+IDSEK-VGEAFGSDTIYLRIVSLDAGGRTENNA-V---KIVLPVLS---S\n+IVVVLSISFVWFKIKDKKRNRGKHRKLVLDGASKSDDIGEGNPAHDLEFP\n+FV-RFEDI-ALATHDFSE-SYKIGQG-GFGKVYKAVLG--DQEVAVK-RL\n+S-RDSQQGTE-EFRNEVI-LIAKLQH-RNLVRLLGCC-VEGDEKLLIYEY\n+LTNKSLDSTLFDVSRKLKLDWTTRFNIIKGVARGLLYLHQDSRLTIIHRD\n+LKAANILLDAEMKPKI--ADFGM-ARI-----------------------\n+-----F-GDNQQNA------------------------------------\n+--------------------------------------------------\n+-----NTRRVVGTYVIKFKPFSVTLVIGMGNSGYMAPEYAMEEVVTGIRR\n+SSTSNIMGFPNLIVYSWNMWKEGKTKDLVDSSIMDSCLM-----------\n+--------------------------------------DE-ALLCVHVAL\n+LCVQEN--PDDRPVMSSVMYILENGCSTELPSPSCPGYFAQRSYVIEQLR\n+ENVQSSTNNFTLTDIEGSASSTIFIVLLLPGLC--ASA----GNKIELGE\n+Q---LLP----GQ--TR----------------------------ASEG-\n+--G-AFVLG----FFSPSNS-T-PA--RQYVGIWYSNIP--DRTVVWVAN\n+RATPEITDPSSAG-SSFAPRLALT---------NDSNLVL-S-----D-A\n+G------GRVL-WTTNVTG-------VAAGASSP-PAAELLNSGNLVIRL\n+--NGV------------IVWQSFDHPTDTFIPEMKVTLNKRTRRGARIVS\n+WQDA-GDP-SPGSFSYGLDPDTSLQLVMWN--GSRPYWRTTVWTGY-LTS\n+AQFLSG-GTT--IYLDVVDT--EEEFYMKLRA-SD------GASPTRYVV\n+TSS----GK-FQLLSWSSKSSE--WITFDSFPTHQCSVYGYCGPYGYCDF\n+T-GAVSTCKCLDGFEPASGDEWSAGRFSGGCRRKEALPCDG---------\n+-GGGHGFLELPRVKVPDRFVMFVE--NMTFDECAERCRRNCSCEAYAHAN\n+LLGVDSRLEAGRRKGGIARCLVWTGELVDMSIIGNTTWGPAAETLYLRVP\n+ANST-----------------GS--RA-R--RNVVKIVMSVL----AS-A\n+-----LMLS--CIF---FCFYKFRENR-RRKE-SQKR-------------\n+---------------------L-I-P-GSGNTSHE-LL-EDN-P-TQDLE\n+FPSIRFSDIVAATDNFSKSFFIGRGGFGKVYKVTLENGQEVAIKRLSEDS\n+DQGIEEFKNEAILIAKLQHRNLVRLLGCCTEGLEKLLIYEYLPNKGLDAI\n+LFD--SARKSLLDWPTRFGIIKGIARGLLYLHQDSRLTVIHRDLKASNIL\n+LDAEMRPKIADFGMAKIFGENQQKANTKRVVGTYGYIAPEYSTEGSFSIK\n+SDVYSFGVLLLEIVSGIRISSTDIMEFP-SLIVYAWSLWKEGKAKNLIDS\n+T-IV-E----S----C-LLDEV-LLCIHVGLLCVEDNPNSRPLMSSVVSI\n+LENGSGVFLAMPNQPAYFTQTT-----------SEMDKM-----TDENSR\n+NTMTI----TA---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----FQG------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------R\n+>3711.Bra027089.1-P\n+--------------------------------------------------\n+--------------------MCTRLLLC--------GHAYYIQSNSLNKE\n+DAHEAINSSSPLSIRQT---------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------LSS-PGGFYELGF-FSPNNTGN-QYIG--IWFKKIVP\n+--RVIVWVAN--RDKPVTS--SAANLT-ISRNGSLILVDEKQA-VIWSTG\n+EA---SFP-SSRSHA-ELLDTGNLVLIDDV-SRTT--IWESFEN-LGNTM\n+LPQSTLMYD-LSHGKKR-ELTSW--KSYSDPSLGN--FSLEI-TPQVPLQ\n'..b'QGLNEFQNEVKLIAKLQHRNLVKLLGCSIQKDEKLLIYELMPNRSLDHF\n+IFD--STRRTLLDWVKRFEIIDGIARGLLYLHQDSRLKIIHRDLKTSNVL\n+LDSNMNPKISDFGMARTFGLDQDEANTNRIMGTYGYMPPEYAVHGFFSVK\n+SDVFSFGVIVLEIISGRKIRGFCDPYHNLNLLGHAWRLWTEKRSMEFIDD\n+L-LD-N----S----A-RLSEI-IRYIHIGLLCVQQRPEDRPNMSSVILM\n+LNG-EK-LLPEPSQPGFYTGKVHSTM-----TESSPR-N-----TDAYSF\n+NEISN----SL---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----LEAR-----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n+>3847.GLYMA12G17450.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------M-------------------------------------\n+--------------------------------------------------\n+--------------------------------------IC-KQVG----H\n+--------RTQ---------------------------------------\n+-----------------------------------TLR----L-----K-\n+-FMSL-I--------LIY----------------------------NIR-\n+-----NPFG---------YS----H--KRYVGIWYKNIP--IQTVVWVAN\n+KANPINDS---SG------IITLN---------NTGNLVL-TQN------\n+---A---YL-V-WYTNNSH---K------QAQN-PVV-VLLDSGNLVIKN\n+--EEE----TD-PE--VCLWQSFDYPSDTLLPGMKLERNIRTGHEWKLTS\n+WKNP-NDPS-PGDIYRVLELYNYPELYVMK--GKKKVYRSGPWNGLYFSG\n+LPYLQN-NTI--FGYNFVSN--KDEIYFTFNL-LN------NCIV-----\n+-----------YRYVWLEGDHN--WTMHRSYPKEFCDNYGLCGAYGNCII\n+NQ--AQGCQCLKGFSPKSPQAWASSDWSQGCVRNKPLSCNG---------\n+-EHKDGFVKFEGLKVPDTTQTWLD-KTIGLEECRVKCLNNCSCMAYSNSD\n+IRGA------------GSGCVMWYGDLIDIRQFE-----TGGQGLHIRMS\n+ASES-V---------------------TN---------------------\n+----------------------------Y---------------------\n+-------------------------------------S-KDK-S-EKDID\n+LPTFDFSFISNATNDFSQSEKLGQGGFGSVYKGILPDGQEIAVKRLSKTS\n+GQGLDEFKNEVMLIAKLQHRNLVKLLGCSIQQDEKLLIYEFMPNRSLDYF\n+IFD--STRHTLLGWTKRFEIIGGIARGLLYLHQDSRLKIIHRDLKTSNVL\n+LDSNMNPKISDFGMARTFGLDQDEANTNRVMGTYGYMPPEYVVHGSFSVK\n+SDVFSFGVIVLEIISGKKNRAFYDPHHHLNLLGHAWRLWIEKRPTELMDD\n+L-VD-N----S----A-CPSEI-IRYIHIGLLCVQQRPEDRPNMSSVTLF\n+LNG-EK-LLPEPNQPGFYTGKAHPTK-----PNSSSR-N-----IDVYSF\n+NEMSN----SL---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----LEPR-----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,960 @@\n+>88036.EFJ07250\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+M---HRY-------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------ICAGCNQEIGPGRFLSCLGSVWHPQCF\n+RCKACGDPISGSQFALSGSDRYHKECYRDLYHPKCEVCHQFIPPNSSGLI\n+EYRAHPFWGQKYCPLHEKDSTPRCCSCERVE-------------------\n+--------------------------ARDARFVSLDDGRKLCLECLDSAV\n+MDTHECQHLYHEILDFYEGMNMKISQSIPMLLVERQALNEAREHERDGYH\n+HLPETRGLCLSEEQTVSTVYRK-PKASRSNPVGSMRKESLRLRRQCEVTA\n+ILVLYGLPRLLTGSILAHELMHAWLRLNGELPELLNPAVEEGICQVMAHT\n+WLESQIGSSG----GSS--------------SSS-SGGKQKPKSINNDRF\n+QEFFLHQIAMDSSPAYGDGFRAGHQSVVQFGLSRTLEHIKLTGSFPV--\n+>88036.EFJ07867\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+M---HRY-------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------ICAGCNQEIGPGRFLSCLGSVWHPQCF\n+RCKACGDPISGSQFALSGSDRYHKECYRDLYHPKCEVCHQFIPPNSSGLI\n+EYRAHPFWGQKYCPLHEKDSTPRCCSCERVE-------------------\n+--------------------------ARDARFVSLDDGRKLCLECLDSAV\n+MDTHECQHLYHEILDFYEGMNMKISQSIPMLLVERQALNEAREHERDGYH\n+HLPETRGLCLSEEQTVSTVYRK-PKASRSNPVGSMRKESLRLRRQCEVTA\n+ILVLYGLPRLLTGSILAHELMHAWLRLNGELPELLNPAVEEGICQVMAHT\n+WLESQIGSSG----GSS--------------SSS-SGGKQKPKSINNDRF\n+QEFFLHQIAMDSSPAYGDGFRAGHQSVVQFGLSRTLEHIKLTGSFPV--\n+>88036.EFJ33296\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------MKWF-DKIFKPLHQK-VHE\n+I---SHNS------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------SS-EA--\n+--D--EELDRAIALSL------SDH------YDDKPAAR-----------\n+--------------------------------------------------\n+--------------------------------DKGATDNDEALARALQES\n+FISEGPS----------------------------------G--FS--SG\n+FSSGFPFGGDGRTRRF---SGAHVCARCKKTIGPGRFLSCMGGLWHPECF\n+RCTSCNKPISGSEFSVSGNDPYHKDCYKELFHPRCDVCNLFIPPNYSGLI\n+EYRVHPFWGQRYCPSHEDDNTPRCCSCERLE-------------------\n+--------------------------TKNSKYVVLDDGRKLCLECMDSAV\n+MDTNEGQPLYQEIINFYEGMNMKITQQIPMLLVERQALNEARAHESNGH-\n+HLTETRGLTLSEEQTVTSVFRR-PRS--RGFFGEMRTESMKLRRNCEVTA\n+ILVLYGLPRLLTGSILAHELMHAWLRLNG-YPSHLNPVVEEGICQVMAHT\n+WLESQIGSS-------S--------------SSSHGAAKPAPHQFDTSKL\n+REFVMHQIAMDPSPAYGDGFRIGQSAVVQFGLPRTLDHIKLTGDFPVS-\n+>88036.EFJ15933\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------'..b'PSHEVDGTPRCCSCERME-------------------\n+--------------------------PRESRYVLLDDGRKLCLECLDSAV\n+MDTNECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKAGHH\n+HLPETRGLCLSEEQTVSTILRR-PRM-AGNKIMGMITEPYRLTRRCEVTA\n+ILILYGLPRLLTGSILAHEMMHAWLRLKG--YRTLSPDVEEGICQVLAHL\n+WIESEIMAGSGSGAASS-----SSG-----SSSSM-SSKKAGRSQFEHKL\n+GDFFKHQIETDTSMAYGEGFRAGNRAVLQYGLKRTLEHIRLTGTFPF--\n+>3218.PP1S395_19V6.3\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------MAIVARRDRMGWGLSRASEGGR-R----\n+GR---ECR----GVGFSASYRYDQGFEYPRPE-------YMPR------Q\n+-SSGG-WHGPNIFDDARPIGVGSSYSNDRHGYDRHHELRP----------\n+---PKYD------------------------RPSYER--------GEP--\n+--SS-EETDRAIAIALS----EDEY------QSAKRGGR-----------\n+--------------------------------------------------\n+--------------------------------PVNNLDEDEQLARAMQES\n+LNFGHRD----------------------------------P--YA--Y-\n+-------SSSYAPPPS-RSSGMNVCAGCGESLGFGRFLSCLGKNWHPNCF\n+CCKKCNNAIAEREFSVQGNEAYHRECYKEIFHPKCEVCNHFIPTNPAGLI\n+EYRSHPFWNQKYCPRHERDGTPRCCSCDRIETGEPG--------------\n+--------------------TYISLAQITGAQGSLADDRKVCLECYDTIV\n+VDNQACQPLYREILKYYRSINMPIAQEIPMLLVARSALNAARDGEKDGHT\n+HNAETRGLCLSEEQTITTVYGG-GK--SRNPMRYLRTEKQKLTRHCEVTA\n+ILVLYGLPRLLTGSILAHELMHAWIRLQGN-FRPMAPHVEEGICQVMSHI\n+WLTAELKKLKGARSS----------------------SNS--SAAIEARL\n+GEFYLHQISSDSSPVYGDGFRHGMAAVQQFGLERVLDHLRLTGNFPL--\n+>3218.PP1S265_4V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------MAWL-GRLFDTPG------\n+----------------SSTYHYREGDAYTQYS-------NVPH------R\n+-SYEG-WQGPSIFSEPRREEWAS-NVEEKPSDSNSSQPSYPSDIPLYSYN\n+IPLNSYDEPS-YSNDSSPYEIVAQSPPNTNDTRTYHNERVSYPQIDAE--\n+--SI-EATNLAIALSLS----EEED------RRR--RSR-----------\n+--------------------------------------------------\n+--------------------------------DVPNTEDDESLARALQES\n+IYLEQSA----------------------------------P--RKIPA-\n+-------KPPGFRPIVQNPNRTNPCAGCKKPLGYGRFLSCLGKNWHPSCF\n+ACKLCSRPIAEREFSVQEGEPYHRDCYKELFHPKCEVCLQFIPTNAAGLI\n+EYRSHPFWNQKYCPKHEADGTPRCCSCDRVE-------------------\n+--------------------------THDEQYVPLADGRKLCLECLETAV\n+FDTKECQPLYREILKFYKNVGMMIDQEVPMLLVERSALNDAREGEKEGMH\n+MTSETRGLCLSEEQTITTVFGGKPVFSRG--PWSLWTEPRQLRRHCEVTA\n+ILVLYGLPRLLTGAILAHELMHAWLRLTGG-FPHMSPEVEEGICQVMSHI\n+WLSAELKRSQNRTST----------------------NA---TSPAQERL\n+GKFYLHQIANDTSPIYGNGFRRGLKAVNYHGLVRVLEHLRMTANFPPGP\n+>3218.PP1S38_163V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------MAWL-GRLFDAPS------\n+----------------SSTYRYHEGDEYPDYT-------NIPR------Q\n+-SHGG-WQGPNIFQDSRSIEGSSSYSEEMPSYTNSIRPSYSSDMPLHAYN\n+IPYNSDDGPS-HSYDRFPYEIVAPPPANTNDTPTYHNERISYPQIDAA--\n+--SM-EATDHAIALALS----EEEN------RGS----K-----------\n+--------------------------------------------------\n+--------------------------------HMPSTDADEELARALQDS\n+LDLQYRA----------------------------------S--RK--E-\n+-------KSPSTRPAVLKPTATNICAGCKQPLGYGRFLSCLGKNWHPHCF\n+ACKMCSKPIDDREFSVQGGDPYHRNCYKELFHPKCEVCLEFIPTNEDGMI\n+EYRSHPFWNQKYCPSHEIDGTPRCCSCDRIE-------------------\n+--------------------------TGEVKYAGLEDGRKICLECLETAV\n+FDTKECQPLYREVLKFYKNVGMMIDQEVPMLLVERTALNEAREGEKEGIH\n+MTSETRGLCLSEEQTVTTVFGGKSS--FPRLSFNFWTEPKHLRRHCEVTA\n+ILVLYGLPRLLTGSILVHELMHAWLRLAGG-FPRMRPEVEEGICQVMSHI\n+WLSAELKRAEKKDST----------------------SAKGITSPAQERL\n+GKFYLYQISSDTSPVYGDGFRQALASVNRYGLVRVLEHLRMTANFQV--\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.066.AA.strNOG.ENOG411BDUE.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.066.AA.strNOG.ENOG411BDUE.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,560 @@\n+>4558.Sb06g034040.1\n+--------------------------------------------------\n+---------------M-KS-SR-------FLFLC----AMFCLMARLGAA\n+NVVLMGNNLTLSFDDIEASFSPGVKGSGVSGVVYASEPLNACSPLTIKTV\n+NGP--P-SPFALIIRGGCTFDEKVKNAQDAGFKAAIVYDNKNSGVLVS--\n+--------------------MAGSSSGIHIYAVFVSKASGEVLKKFSGNM\n+DVEVWILPTFENSAWSIMAISFVSLLAMCAVLGTCFFVRRHRIRREHPRI\n+AEDREFHGMSSQLVKAIPSLIFTKVQEDNCTSSMCAICLADYNVGEKLRV\n+LPCRHKFHAACVDLWLTSWRTFCPICKRDARSGASEVVATEATPLLSSAA\n+RLP---------------------------------SFRSSVAA------\n+---------------------SPPRPIS---RHPS-SHSVSRAYSVS--S\n+TPNSPNPFISSH-ISSPG-IRASRSITDLGNIS-SLHP------RISHLS\n+--ST-HSLVGSHLSPPISIR--YW-SSHVAHSGYGSPSPHVSSSYISNSG\n+YGSSSYCYLGLGGSSHSQHGTYLRRCGESGPSLCTMVPQ-----QLQWET\n+--------------------------------------------------\n+--NVAAGASSAKSLRQSSYLRHCGDSDASLSDMTSA-QSLPRC\n+>4555.Si021801m\n+--------------------------------------------------\n+-------------------------MKSRFLFLC----VMVCLMAQLGAA\n+NVVLMGNNLTLSFDDIEASFAPGVKASGVNGIVYAAEPLNACSPLTINAV\n+EGL--P-SPFALVIRGGCAFDEKVKNVQDAGFKAAIVYDNENSGVLVS--\n+--------------------MAGSSSGIHIYAVFVSKASGEVLKKFSGHT\n+DVEVWILPTFENSAWVIMAISFISLLAMSAVLATCFFVRRHRIRRDHPRN\n+LEAREFHGMSSQLVKAMPSLIFTKVQEDNCTSSMCAICLEDYSFGEKLRV\n+LPCRHKFHAACVDLWLTSWRTFCPVCKQDASSGVSELAATEATPLLSSAV\n+RLPSQS---S--------------------------SSRLSVAA------\n+---------------------SPPRPIS---RRPS-SHSVSRAYSVS--S\n+TPQSPNPFRSYT-NSPG--ISTSRSNADLANMS-SPHP------RISHLS\n+--ST-HSLVGSHLSPPISIR--YS-SPHVSQFGHGSPSVHVGSSYMSNSL\n+YGSSSYYYLGA----SSQHGSYLRRCGESGPSLSTMVPQ-----SPQQSQ\n+---L----------------GHGGES-----------------------S\n+EANVTAGASSAQSLQQ-SYLRHCGDSDASLSDMMSA-QSLPGC\n+>4577.GRMZM2G003656_P01\n+--------------------------------------------------\n+-------------------------MKSRFLVLC----AIVCVMAQMGDA\n+NVVLLGNNLTLSFADIEASFSPGVKGSGVNGIVYASEPLNACSPLTIKAV\n+KGP--P-SPFALIVRGGCTFDEKVKNAQDAGFKAAIVYDNENSGVLVS--\n+--------------------MAGSSSGIHIYAVFVSKASGEVLKKSSGHT\n+DVEVWILPTFDNSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRDHPRI\n+PEAREFHGMSSQLVKAMPSLIFTKVQEDNCTSSMCAICLEDYSVGEKLRV\n+LPCRHKFHAACVDLWLTSWRTFCPVCKRDATSGVSELPATEATPLLSSAV\n+RLPSQP---S--------------------------SFRSSVAA------\n+---------------------SPPRPIS---RHPS-SHSVSRAYSVS--S\n+TPHSPNPFRSHT-NLPGV-IHASRSTTDLANMS-SPHP------RISHLS\n+--SSTHSLVGSHLSPPISIR--YP-LPH---SRHESPSPHVSSPYISNSG\n+YGSSSYYYLGG----SSQHGSYLRRCGESGPSLSTMVPR-----SSQQ--\n+-----------------QFQ-----------------------------S\n+EANVAAGASSAQSSRQ-SYLRRCGDSDASLSDMASA-QSLPGC\n+>4558.Sb08g021220.1\n+--------------------------------------------------\n+------------------M-AT-AQIKSRFLVLY----VIVCLMAQMGDA\n+NVVLLGNNLTLSFDDIEASFSPGVKGSGVNGVVYASEPLDACSPLTIKAV\n+KGP--P-SPFALIVRGGCTFDEKVKNAQDAGFKAAIVYDNENSGVLVS--\n+--------------------MAGSSSGIHIYAVFVSKASGEVLKNFSGHT\n+DVEVWILPTVENSAWSIMGISFISLLAMSAVLATCFFVRRHRIRRDHPRI\n+PEAREFHGMSSQLVKAMPSLIFTKVQEDNCTSSMCAICLEDYSVGEKLRV\n+LPCRHKFHAACVDLWLTSWRTFCPVCKRDAMSGVSEFPATEATPLLSSAV\n+RLPSRP---S--------------------------SFRSSVAA------\n+---------------------SPPRPIS---RHPS-SHSVSRAYSVS--S\n+TPQSPNPFRSRT-NLPG--IHTSRSTADLANMS-SPHP------RISHLS\n+--SA-HSLVGSHLSPPISIR--YS-LPQLAQSGHGSLSPHVSSSYISNSG\n+YGSSSYYYLGG----SSQHGSYLRRCGESGPSLSTMAPQ-----SPQQFQ\n+SEANVVAGTSSAQSFRQSYLRHCGDSDASLSDMMSAQSLPQQF-----QS\n+DANVAAGASSAQSLRQ-SYLRRCGDSDASLSDMTSA-QSLPGC\n+>4533.OB03G15100.1\n+--------------------------------------------------\n+------------------M-NR-RRAMLLLICLC----ATFCIMTQLGAA\n+NVVLMGTNLTLSFDDVEASFAPGVKGSGFEGIVYTAEPLDACSPLTSKAE\n+KGS--P-SPFALIIRGGCTFDEKVKNAQDAGFKAAIVYDNENSGVLIS--\n+--------------------MAGSSSGIHIYAVFISKASGEVLKKFSGHT\n+DVEVWILPAFENSAWSIMAISFISLLAMSAVLATCFFVRRHHIRRDRPRV\n+PEAREFHGMSSQLVKAMPSLIFTKVQEDNCTSSMCAICLEDYNVGEKLRV\n+LPCRHKFHAACVDLWLTTWRTFCPVCKRDASTGISDPPASETTPLLSSAV\n+RLPSQS---S--------------------------SFRSSVAA------\n+---------------------SPPRPIS---RRSS-SQSISRIYIAS--G\n+TPHSSNPLRS-Y-TNSPA-LSISRSNVDLSNMS-SSRP------RTSHLS\n+--SA-HSLVGNHLSPPINTR--YA-SPYVSRSGHASPSPHVTSSYVSNSG\n+YG-SSSYYLGSSS--QH--RPYLRRCGESGPSLSTMAPQ-----SPQQFQ\n+---L----------------RHGGESDINLPGPSSSQSFRQSYLRHCADS\n+EINL-AGASSGQSFRQ-SYLRHCADSDASLSAMASA-QSLPGC\n+>39946.BGIO'..b'--------------------------------\n+>3847.GLYMA20G31460.1\n+--------------------------------------------------\n+--------MFFNQKIV-LF-KSFALMGTSNL----LLFFSLMSLCAMAAS\n+KVVLIGNNITLSFDDIEANFAPAVKGSGKYGVLYLAEPLDACAELTNKVE\n+QLPNAS-SPFALVVRGGCSFEEKVRIAQKAGFKAVIVYDNEEGGILV---\n+-------------------AMAGNSAGIRIHAVFVSKASGEILKKYAGLT\n+NVEIWLIPTFENSAWSIMAISFISLLAMSAVLATCFFVRKHRIRRERPRA\n+SLVREFHGMSSRLVKAMPSLVFTSVLEDNCTSRTCAICLEDYCVGEKLRI\n+LPCCHKFHAACVDSWLTSWRTFCPVCKRDARTGLTDPPPSESTPLLSSTP\n+ASMASS-VLSSARSSLASSSAIQIARTASMASSALPSARSSLAS-SSAIQ\n+IARTASMASSALHSARSSLASSSAIQIS---RAASQTPSVSRNHSIA--S\n+TPYVQPSLRSS-YHQSPS-LSISRSSVDLRNA-------S-QRSLASHLN\n+--SP-CSMGYPSLS-SLNSR--YM-SPHIPSPSNASVS-YMGS-------\n+---------------SSH-QQHPLRYSESAASFSPFASTHSLPEC-----\n+--------------------------------------------------\n+-------------------------------------------\n+>88036.EFJ36028\n+--------------------------------------------------\n+------------------------------LLLV----VLTLVLGRASAM\n+VVLITAKNETLPFPDMEASFAPRVPASGISGLFYEAYPLNACDAIINGPG\n+LLIGSI-PVFAIVERGGCKFDEKILNAQDAGFSAVIVYNNEEGHDLIS--\n+--------------------MSGSSDDVHIPAVFVSKSAGETLLEYSKQI\n+GARCYILPAIENTAWSVMAVSFISLLAVTAVLTTFLFVRRYRLRHLGSRL\n+LLLRDSYGMSAREVKALPTVIFKCLGDGQGTSDTCAICLEEYESGEKLRV\n+LPCHHDFHAACVDQWLTTRRPFCPVCKRDAHNKNEEPPPSESTPLLA---\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>88036.EFJ06163\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------LSA---PRVPASGISGLFYEAYPLNACDAIINGPG\n+LLIGSI-PVFAIVERGGCKFDEKILNAQDAGFSAVIVYNNEEGHDLIS--\n+--------------------MSGSSDDVRIPAVFVSKSAGETLLEYSKQI\n+GARCYILPAIENTAWSVMAVSFISLLAVTAVLTTFLFVRRYRLRHLGSRL\n+LLLRDSYGMSAREVKALPTVIFKCLGDGQGTSDTCAICLEDYESGEKLRV\n+LPCHHDFHAACVDQWLTTRRPFCPVCKRDAHNKNEEPPPSESTPLLA---\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>3218.PP1S58_112V6.1\n+----------------------------------------MRQSRQWRMV\n+PFTDVCGCGRGLVSRI-MN-HRELMISLAGLSLV----LLTLLLGRVNSA\n+VILLTESNESWSFPDTEASFSPRIPTTGIVGVLHASNPLDACSPLTNVSR\n+QGQTLF-SDFLLVERGVCNFEVKVWNAQEAGFEAVIIYNNQNDHELVT--\n+--------------------MSGSSNDIHAYSVFVSKVTGEFLLKYADDK\n+GATCYIMPAFENTAWSVMAVSFISLLAVSSVLVTFFFVRQHRIQHLSARF\n+L-PKEPAGMSVKEVNTLPSFVFKHIEDGKGTSETCAICLEDYVAGEKLRL\n+LPCQHEFHLDCIDQWLTTRKPFCPVCKRDAQSKVDKPVATETTPLLAAVG\n+RALGVGES----------------------------RVGTPMN-------\n+---------------------SSPLFAP-TGASPD-ETTDTRIFSLS--S\n+P-D---------------------GSEDLC--------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n+>3218.PP1S28_303V6.1\n+--------------------------------------------------\n+--MPSVVAEAGFASRI-MS-YREIMISLAGLCLV----LLTLLIGRVNSA\n+VILLAGTNETWSFPDVESRFAPRVPTAGVGGVLYASNPLDACSPLLNVST\n+PGKGSA-PAFLLVQRGVCNFEIKVRLAQEAGFAAVIVYNDQDDRELVT--\n+--------------------MSGNPVNIHAYAVFVSKYSGEFLLKYAGDV\n+GATCHIMPAFENTAWSVMAVSFISLLAVSSVLATFFFVRQHRLRHLSARY\n+L-LREPAGMSVKEVNALPSLIFKCVEDGKCTSETCVVCLEDYIPGERLRL\n+LPCQHEFHLDCIDQWLTLRKPFCPVCKRDAQSQVHEPVATETTPLMAAVG\n+RALGGGSI----------------------------RVGTSILSAR----\n+---------------------SSPLFTTSVINSPN-DTPDTRIFSLS--Y\n+P-D---------------------GGEDLC--------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.067.AA.strNOG.ENOG411BDX3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.067.AA.strNOG.ENOG411BDX3.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1050 @@\n+>3218.PP1S12_244V6.1\n+MRL-----------CS------ESTLTRAWLSRGTRHE------------\n+--------------------------HNEGVFDYLDANHLNDDSMQPEKR\n+LAVCPLLLENNAMAYQYYPGSTRYE--------------ATGG-A-LVDG\n+QFRHANFMQPS----DL--VQH----LEQ--LHSVLG------TVSQ--D\n+SPNIPAHHTLDAGAQTSNNRTSDL---AGWID-GMIDELSFNNAGTMAAP\n+QQRSLTED------S-L--------------HQNELEASSSH--DSSLDT\n+GSSRLPTLHYQN---T-----------------------PAVGNNFLATP\n+QNDA-------------------------SQLNANRAT--GAVLEQQPSP\n+MGEDEDNGVRLVHSLLACAESIQRGNLNLAEQTLRRIQLL--S----LPP\n+GPMGKVATHFIDALTCRIYGVA---------------F---------SSG\n+-NNV--GSNQSDSLSELLHFHFYETCPYLKFAHFTANQAILEAFAGQKQV\n+HVIDFNLMHGLQWPALIQALALRPGGPPRLRLTGIGPPQSG-GSDVLQEI\n+GMKLAQLAETVKVEFEFRGVVAVKLDDIKPWMLQIC---------HG--E\n+AVAVNSVFQLHKLLY-------------------SAG--------S-VIP\n+IDEVLRSARALKPKIFTIVEHEANHNQPSFLGRFTEALHYYSTMFDSLEA\n+CSLP------------------SD---SSEQVLAEMYLGREINNIVACED\n+AARVERHENLVQWQMRMLKAGYRPIQLGLNAFKQASMLLTMFS-GDGYRV\n+EEKLGCLTLGWHTRPLISASAWQCLLHKAHTAVTGPNLFEVVLRWSMNN-\n+DGVG----VSSQPSVDLSPAGFPERLPHDLRMELVYCWKENSILSFTVKA\n+SNLVKNEQLGWKSPLAAEIPLPVTKSEQDQHFR\n+>3218.PP1S175_16V6.1\n+MCP-----------GH------ELTLTYVCLAPWAYDHSH---RHLLHKA\n+I---------PLKLDSQQEL-HMAYQYSPGGSRWKPTGGTLV-----DGR\n+LRHDKFTQAS----------------------------------------\n+---------------DA--VQQ----LEE--LHTSLG------SVSQ--D\n+SLNIPAYYTLGSSSQAVSNCSTDL---AGWID-CMIEELSSNTACPIMAP\n+QQQHGLLE------G-S------------F-LKNDHDASSCR--DS----\n+------LLETGSHRLS-NVQFQD------T---------SAARNKSSTAP\n+HNGT-------------------------SQVNAIRTT--AAGLEQQLNK\n+MGEDENNGIQLVHSLLACAESIQRGNLSFAEETLRRIELL--S----LPP\n+GPMGKVATHFIGALTRRIYGVA---------------S---------SSG\n+-NNS--SSNQSDSLLGLLHFYFYESCPFLRFAHFTANQAILEAVTGLKEV\n+HVIDFNLMQGLQWPALIQALSLRQGGPPRLRLTGIGPPQPS-GSDTLQEI\n+GTKLAELAKTVRVDFEFRGVIAVKLDDIKPWMLQIR---------HG--E\n+AVAVNSVLQLHKLLY-------------------SAG--------P-EAP\n+IDAVLLLVRELKPKIFTIVEHEANHNQPSFLGRFIEALHYYSTMFDALEA\n+CNLP------------------SE---NNEQVLIEMYLGREIYNIVACED\n+GARTERHENLFQWRLRLLKAGYRPIQLGLNAFKQASMLLTMFS-GEGYRV\n+EEKLGCLTLGWHSRPLIAASAWKCA-------------------------\n+--------------------------------------------------\n+---------------------------------\n+>3711.Bra031991.1-P\n+MK----------R-GH------GETWDPAPQSQQPSG-------------\n+--------------------------------------------------\n+-----------------SCEGSSSVVDNIK------GKMADDS---NMDE\n+LLEVLGYKVRSSEMAEV--AQK----LEQ--LEMVLS------N------\n+-DDVGSTVL--ND--TVHYNPSDL---SNWVE-TMLSELNNPEPSDLDP-\n+------------------------------------TRICED--RSEYGL\n+SAIPGLSAFPKA---EEGAEEEA------------SSKRIRLE-------\n+-------------------------SV------------GSWGELTRPVV\n+VVDSQETGVRLVHALVACAEAIQQQDLNLADALVKSVGTL--AA---SQA\n+GAMGKVATYFAQGLARRIYAAD---------------L---------SG-\n+------GSSVGPSFEEALQMHFYESCPYLKFAHFTANQAILEAVTTARRV\n+HVIDLGLNQGMQWPALMQALAVRPGGPPSFRLTGVGPPQTE-SSDSLQQL\n+GWKLAQFAQAIGVEFEFKGLAAESLS------------------------\n+----------------------------------RT------------GD\n+VRD---------PARIGNI-SEANHNGVVFLDRFNEALHYYSSLFDSLED\n+SYTL-------------------P---SQDRVMSEVYLGRQIVNVVAAEG\n+TDRVERHETLAQWKARMGSVGFDPVPLGSSAFKQASMLLSVFAGGDGYRV\n+EENDGCLMLGWQTRPLIATSAWKLAGA-----------------------\n+--------------------------------------------------\n+---------------------------------\n+>59689.fgenesh2_kg.3__292__AT3G03450.1\n+MK----------R-GH------GETWDPP----PASR-------------\n+--------------------------------------------------\n+-----------------SREGPSMADKKKV-----AD-DNNN----MDDE\n+LLAVLGYKVRSSEMAEV--AQK----LEQ--LEMVLS------N------\n+-DDVGSTVL--ND--TVHYNPSDL---STWVE-SMLSELNNPTSSDLDP-\n+------------------------------------TRSCVD--RSEYDL\n+RAIPGLSAFPKE---EEVFDEEA------------SSKRIRLG-------\n+-------------------------SWC-----------ESAGESTRSVV\n+LVDSQETGVRLVHALVACAEAIQQENLNLADALVKRVGTL--AA---SQA\n+GAMGKVATYFAQALARRIYRDY---------------T---------AE-\n+-TDV--SG---GSFEEVLQMHFYDSCPYLKFAHFTANQAILEAVATARRV\n+HVIDLGLNQGMQWPALMQALALRPGGPPSFRLTGIGPPQTE-NSDSLQQL\n+GWKLAQFAQNMGVEFEFKGLATESLSDLEPEMFETR---------PD-SE\n+TLVVNSVFELHRLLA-------------------RS------------GS\n+IEKLLNTVKAIKPSIITVVEQEANHNGIVFLDRFNEALHYYSSLFDSLED\n+SGSL-------------------P-'..b'GYKVRSSELQHV--AEN----MER--LENVMD------I--VNSS\n+TNNNISQLA--SD--TIFYNPSDI---GSWID-TLLSEFDQTASLPYDF-\n+--------------------------------SE------L--PDLDT--\n+--------------------------------------------------\n+----------------------------------------DQIQNLKPTL\n+VTMEEDSGIRLVHTLMTCADSVQHGDLPFAGSLIENMQGLLAHV---NTN\n+IGIGKVAGYFIDALRRRIFAQG---------------VF--------L--\n+----T--SCSYPIEDDVLYHHYYEACPYLKFAHFTANQAILEAFNGHDCV\n+HVIDFNLMQGLQWPALIQALALRPGGPPLLRLTGIGLPSSD-NRDTLREI\n+GLRLAELARSVNVRFAFRGVAAWRLEDVKPWMLQVN---------PN--E\n+AVAVNSIMQLHRLLA-------------------SDSD-------PAGSG\n+IETVLGWIRSLNPKIISVVEQEANHNEDMFLERFTEALHYYSTVFDSLEA\n+CPVE------------------P------DKALAEMYLQREICNVVCCEG\n+PARVERHEPLDKWRKRLGKAGFKPLHLGSNAYKQASMLLTLFS-AEGYCV\n+EENQGCLTLGWHSRPLIAASAWHAAPVQDRETLRFEQ-------------\n+--------------------------------------------------\n+---------------------------------\n+>3847.GLYMA06G23940.1\n+MA------------------------------------------------\n+--------------------------------------------------\n+----------------------S-SSSN-G-----SSSGSKSW-D--IDG\n+DLAGFGYKVRSSELQHV--AEN----MER--LENVMD------I--VNSS\n+TNNNISQLA--SD--TVFYNPSDI---GSWVD-TLLSEFDQTASLPYDF-\n+--------------------------------SD------F--LDLDT--\n+--------------------------------------------------\n+----------------------------------------DQNQNHKPTL\n+VTMEEDSGIRLVHTLMTCADSVQRGDLAFAGSLIENMQGLLAHV---NTN\n+IGIGKVAGYFIDALRRRILGQG---------------VF--------Q--\n+----TLSSSSYPYEDNVLYHHYYEACPYLKFAHFTANQAILEAFNGHDCV\n+HVIDFNLMQGLQWPALIQALALRPGGPPLLRLTGIGPPSSD-NRDTLREI\n+GLRLAELARSVNVRFAFRGVAAWRLEDVKPWMLQVN---------PN--E\n+AVAVNSIMQLHRLLA-------------------SDSD-------PIGSG\n+IETVLGWIRSLNPKIISVVEQEANHNQDRFLERFTEALHYYSTVFDSLEA\n+CPVE------------------P------DKALAEMYLQREICNVVSSEG\n+PARVERHEPLAKWRERLEKAGFKPLHLGSNAYKQASMLLTLFS-AEGYSV\n+EENQGCLTLGWHSRPLIAASAWQAAPMQDRETLRFEQ-------------\n+--------------------------------------------------\n+---------------------------------\n+>3847.GLYMA20G34260.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------MER--LENVI--------------\n+-----------SD--TILYDPSNI-GLGSLVD-TLLSDLDQTMSLPSHY-\n+--------------------------------HL------SSD-------\n+--------------------------------------------------\n+---------------------------------------------LPDFA\n+TTVEEHSGIRLIHTLMTCADSLQRGHFSFAASLIQNMQGLLAHV---NTN\n+CGIGKVAACFIDALRRRISNKF----------------------------\n+----P---ASSAYENDVLYHNYYEACPYLKFAHFTANQAILEAFNGHDCV\n+HVIDFNLMQGLQWPALIQALALRPGGPPLLRLTGIGPPSAE-NRDNLREI\n+GLRLAELARSVNVRFAFRGVAAWRLEDVKPWMLQVS---------PN--E\n+AVAVNSIMQLHRLTA-------------------VK------------SA\n+VEEVLGWIRILNPKIVTVVEQEANHNGEGFLERFTEALHYYSSVFDSLDA\n+CPVE------------------P-----DKAALAEMYLQREICNVVCCEG\n+PARLERHEPLAKWRDRLGKAGFRALHLGFNAYKQASMLLTLFS-AEGFCV\n+QENQGSLTLGWHSRPLIAASAWQAAPLGDDETLRFEH-------------\n+--------------------------------------------------\n+---------------------------------\n+>3847.GLYMA10G33380.1\n+MK------------------------------------------------\n+--------------------------------------------------\n+------------------------MISS-A-----SNENKTVV-D--MDD\n+HLAGLGYKVRSSELCQV--AAN----MER--LENVIS-------------\n+-STDLSQLA--SD--TTLYDPSNI-GLGSWVD-TLLSEFDQTASLPLQY-\n+--------------------------------DF------ATDPNH----\n+--------------------------------------------------\n+-------------------------------------------NKQLALV\n+TTVEEDSGIRLVHMLMTCADSVQRGDFSFAGSLIENMQGLLAHV---NTN\n+CGIGKVAGYFIDALRRRISNTL----------------------------\n+----P--TSSSTYENDVLYHNYYEACPYLKFAHFTANQAILEAFNGHDCV\n+HVIDFNLMQGLQWPALIQALALRPGGPPLLRLTGVGPPSAE-NRDNLREI\n+GLRLAELARSVNVRFAFRGVAAWRLEDVKPWMLQVS---------LN--E\n+AVAVNSIMQLHRVTA-------------------VD------------AA\n+VEEVLSWIRSLNPKIVTVVEQEANHNGEGFLERFTEALHYYSTVFDSLDA\n+CPVE------------------P-----DKAALAEMYLQREICNVVCCEG\n+PARLERHEPLAKWRDRLGKAGFRPLHLGFNAYKQASMLLTLFS-AEGFCV\n+QENQGSLTLGWHSRPLIAASAWQAAPLRDDETLRFGH-------------\n+--------------------------------------------------\n+---------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.068.AA.strNOG.ENOG411BE45.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.068.AA.strNOG.ENOG411BE45.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,360 @@\n+>88036.EFJ08453\n+--------------------------------------------------\n+-----------------------------------------------PES\n+YR------------------------------------------------\n+-----------------GLPLEVGTALARYVSSKVIPQQTFDEIMMTVRV\n+LAARGPCNFLVFGLGFDSVMWKTLNHGGRTVFLEETEDWIKQVTGKNPDL\n+--EAYLVRYNTKLMDAGRLMDHARKNRNGKCR--P---VQAIRNSTCKI-\n+-ALSYLPKKLYEVDWDVIMVDAPRGYFAEAPGRMAAIFSASVMARSRKNG\n+--TTDIYVHDVERPVERQYCEEFLCRANLVEEAPTKRLWHF---------\n+------------------\n+>88036.EFJ15132\n+--------------------------------------------------\n+-----------------------------------------------PES\n+YR------------------------------------------------\n+-----------------GLPLEVGTALARYVSSKVIPQQTFDEIMMTVRV\n+LAARGPCNFLVFGLGFDSVMWKTLNHGGRTVFLEETEDWIKQVTGKNPDL\n+--EAYLVRYNTKLMDAGRLMDHARKNRNGKCR--P---VQAIRNSTCKI-\n+-ALSYLPKKLYEVDWDVIMVDAPRGYFAEAPGRMAAIFSASVMARSRKNG\n+--TTDIYVHDVERPVERQYCEEFLCRANLVEEAPTKRLWHFRLAPQLSGS\n+S----SKSFC--------\n+>88036.EFJ20142\n+--------------------------------------------------\n+-----------------------------------------------R--\n+--------------------------------------------------\n+------------------LPHDLMTALVHYASTDTTPQQTREEILMTAKV\n+LASRGPCNFLVFGLGHDSLLWKMLNYAGRTVFLEESEDWIRQISEKHPEL\n+--ETHIVEYSTVLTEADQLLEHARSNRKGKCT--A---VQNLLLSECKL-\n+-ALNGLADELFQVEWDVIMVDAPRGYFPGAPGRMAAIFSAAVMARSRKTG\n+-NGTDVFVHDVERPVERSYSEEFLC-------------------------\n+------------------\n+>88036.EFJ14267\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------LPHDLMTALVHYASTDTTPQQTREEILMTAKV\n+LASRGPCNFLVFGLGHDSLLWKMLNYAGRTAFLEESEDWIRQISEKHPEL\n+--ETHIVEYSTVLTEADQLLEHARSNRKGKCT--A---VQNLLLSECKL-\n+-ALNGLADELFQVEWDVIMVDAPRGYFPGAPGRMAAIFSAAVMARSRKTG\n+-NGTDVFVHDVERPVERSYSEEFLC-------------------------\n+------------------\n+>39947.LOC_Os12g10320.1\n+MSSPMHVRKAI-HFVS----------------------------------\n+--------------MKAKLQ----SFGGLRLLLVGCLAALLLLFAV-RTL\n+SFT-TSSATAT-AA---REAAE----------------------------\n+-----------AGC--GKLPAAVAQAMVHYATANVTPQQTAAEIGVSLRV\n+LQLRAPCNFLVFGLGLDSAMWAALNHGGRTVFLEEDASWIASVKAGHPGL\n+--ESYHVAYDTRVTDADELIALRHEP---ACT--SQPDLAAAAAASCRL-\n+-ALRGLPPVFHEVEWDLIMVDAPTGWTPESPGRMGAIYTAGMAARARTPG\n+AGATEVFVHDVDRHVEDTFSKAFLCDGYLVEQV--GRIRRFVIPSHRDK-\n+D----GTPFCP-------\n+>4538.ORGLA12G0055200.1\n+MSSPMHVRKAI-HFVS----------------------------------\n+--------------MKAKLQ----SFGGLRLLLVGCLAALLLLFAV-RTL\n+SFT-TSSATAT-AA---REAAE----------------------------\n+-----------AGC--GKLPAAVAQAMVHYATANVTPQQTAAEIGVSLRV\n+LQRRAPCNFLVFGLGLDSAMWAALNHGGRTVFLEEDASWIASVKAGHPGL\n+--ESYHVAYDTRVTDADELIALRHEP---ACT--SQPDLAAAAAASCRL-\n+-ALRGLPPVFHEVEWDLIMVDAPTGWTPESPGRMGAIYTAGMAARARTPG\n+AGATEVFVHDVDRHVEDTFSKAFLCDGYLVEQV--GRIRRFVIPSHRDK-\n+D----GTPFCP-------\n+>39946.BGIOSGA011022-PA\n+MSSPMHVRKAI-HFVS----------------------------------\n+--------------MKAKLQ----SFGGLRLLLVGCLAALLLLFAV-RTL\n+SFT-TSSATAT-AA---REAAE----------------------------\n+-----------AGC--GKLPAAVAQAMVHYATANVTPQQTAAEIGVSLRV\n+LQRRAPCNFLVFGLGLDSAMWAALNHGGRTVFLEEDASWIASVKAGHPGL\n+--ESYHVAYDTRVTDADELIALRHEP---ACT--SQPDLAAAAAASCRL-\n+-ALRGLPPVFHEVEWDLIMVDAPTGWTPESPGRMGAIYTAGMAARARTPG\n+AGATEVFVHDVDRHVEDTFSKAFLCDGYLVEQV--GRIRRFVIPSHRDK-\n+D----GTPFCP-------\n+>4577.GRMZM5G844894_P01\n+MSSPTHARKAI-HLAS----------------------------------\n+--------------LRARLAQQGKAGVALRLLLAAALAGFLLVFAA-RTL\n+VTS-PVPASPS-YS---Y--------------------------------\n+--SSE------PQP--HPLPLPVAEALVHYATSNATPQQTAEEIGVALRV\n+LQRRAPCNFLVFGLGLDSPMWAALNHGGRTVFLEEDAAWIGSVRGRHPAL\n+--ESHHVAYDTALADADALLGLRAHP---ACV--AQPDLAAAAAASCRL-\n+-ALRGLPPVFAGLDWDLVMVDAPTGWTPRAPGRMGAIYTAGMAARARRPG\n+AGPTHVFVHDVDRPVEDAFSRAFLCEGYLAEQV--GRIRHFVIPSHRDK-\n+D----GTPFCP-------\n+>4555.Si010707m\n+MSSPMHVRKAI-HFAS----------------------------------\n+--------------LRARFA-QGKGGLALRLLLAAALAGFLLVFAA-RSL\n+SSP-SPSTSRR-QE---A--------------------------------\n+-AECG------GEG--KGLPLPVAEALVHYTTSNVTPQQTADEIGVSLRV\n+LQRRAPCNFLVFGLGFDSPMWAALNHGGRTVFLEEDASWIANVRSKHPAL\n+--ESYHVTYDTVLTESDALLELRDHP---ACV--AQPDLASAAEASC'..b'H---------K\n+PKGCP----TTQQC--TKMPISLSDALVHYVTSNVTPQQTFDEVSVSKRV\n+LDKKSPCNFLVFGLGHDSLMWASLNHGGRTLFIEEDKAWIETVTNKFPNL\n+--ESYHVVYDTKVKNSDKLMELGRSE---ECT--S---VTDPRNSKCDL-\n+-ALKDFPADFYETKWDLIMVDAPTGYHEEAPGRMSAIYTAGLLARNRED-\n+-GETDVFVHDVNRPVEDEFSATFLCKGYMREQN--GRLRHFTIPSHRAR-\n+T----GRPFCPVDVDRRR\n+>3702.AT4G09990.1\n+--------------------------------------------------\n+--------------MRNKS----QSFISSKLIFICCSILVLFILFLKRAS\n+FSS-NSTATIR-D------------------------EYH---------Q\n+KSKCP---STPQQC--TKLPTSLSDALVHYVTSEITPQQTFDEVSVSKRV\n+LDKKSPCNFLVFGLGHDSLMWASLNHGGRTLFLEEDEAWIETVTKKFPNL\n+--ESYHVVYDTKVKDSNKLMELKRTE---DCK--A---VSDPRDSKCAL-\n+-SLKGFPADVYETQWDVIMVDAPTGYHDEAPGRMSAIYTAGLLARNRYDG\n+-GETDVFVHDINRPVEDEFSVAFLCGGYMKEQQ--GRLRHFNIPSHRAS-\n+F----GTPFCPADISRRF\n+>59689.fgenesh2_kg.6__2979__AT4G09990.1\n+--------------------------------------------------\n+--------------MRNKP----QPIISSKLIFICFSILVLFILFLNRAS\n+FSS-SSTSTIR-R------------------------EYH---------E\n+IPKCP---LTSLQC--TKIPISLSDALVHYVTTEITPQQTFDEISVSKRV\n+LDKKSPCNFLVFGLGHDSLMWASLNHGGRTLFLEEDKAWIKTVTKKFPNL\n+--ESYHVEYDTKVKDSNKLIELERTE---DCK--A---VSDPRDSKCAL-\n+-SLKDFPADVYETQWDVIMVDAPTGYNDDAPGRMSAIYTAGLLARNRYDG\n+-GETDVFVHDINRPVEDEFSVAFLCRGYIKEQQ--GRLRHFTIPSHRAS-\n+L----GTPFCPADISRRF\n+>3847.GLYMA04G43510.1\n+--------------------------------------------------\n+--------------MRSKT---TQFTCTFKVALLSLAVFCLFILVF-RSS\n+IFS-LSPQLTS-QT---NMSSSDTIVPVSPQETE-NAGTP---------S\n+SSSCPNSPPLNPPC--TKAPPSLANAIIHYATANVTPQQTLHEISVSARV\n+LEKKSPCNFLVFGLGHDSLMWTSLNYGGRTVFLEEDKSWIDQIQEKVPSL\n+--ESYHVMYDTQVHQAEELMKTGMKE---DCQ--K---VTDPRFSRCPL-\n+-AHKGLPSEVYDIDWDVIMVDAPTGYFDEAPGRMSAIYTAGLIARNKER-\n+-GQTDVFVHDVDRKVEDMFSKAFLCEGYFKEQE--GRIRHFNIPSHRSR-\n+L----WRPFCPE------\n+>4081.Solyc11g031950.1.1\n+--------------------------------------------------\n+--------------MRSKN----QSPINVKLILIGIILVFLLFLVL-RST\n+YSP-SPDQQTK-SL---VSKSSSS------SQDEE-TDH--------Q-S\n+SEACPS-----NTC--NKISPSLANALVHYATSNVTPQQTLKEISVSLKV\n+LEKKSPSNFLVFGLGHDSLMWTALNHGGRTVFLEEDKSWIEQIQSQLPNL\n+--ESYHVIYDTRITQADELMEIGMSNE--DCK--K---VTDPRLSKCQL-\n+-ALKGLPQQVLEIDWDLIMVDAPTGWHDGAPGRMSAIYTAGLIARNKQE-\n+-GETHVFVHDVDRVVEDQFSKAFLCEGYLLQQE--GRIRHFNIPSHKAR-\n+L----GRPFCP-------\n+>4113.PGSC0003DMT400080082\n+--------------------------------------------------\n+--------------MRSKS----QSPINVKLILIGIFLVFLLFWVL-RST\n+YSP-SPEQQTQ-SL---DHSSVVSKSSS-EDQETD-EDHQSSSPSSSTSS\n+SVACPS-----NTC--NKISPSLANALVHYATSNVTPQQTLKEISVSLRV\n+LEKKSPCNFLVFGLGHDSLMWTALNHGGRTVFLEEDKSWIEQIQSQLPNL\n+--ESYHVIYDTRITQADELMEIGMSNE--DCK--K---VTDPRFSKCQL-\n+-ALKGLPQQVLEIDWDLIMVDAPTGWHDGAPGRMSAIYTAGLIARNKLD-\n+-GETDVFVHDVDRIVEDQFSKAFLCESYLVEQE--GRIRHFNIPSHRSR-\n+L----GRPFCP-------\n+>29760.VIT_00s0238g00020.t01\n+--------------------------------------------------\n+--------------MRPSK---PQTSINLKLILVCFLCLLLFLLVF-KSN\n+FTP-FQENHPS-PI---LETHVSNSTS---TPA--AEEQP---------P\n+SRDCPS-LPLTPTC--TKTPPSLAQALVHYATLNITPQQTFNEISVSLRV\n+LQKKAPCNFLVFGLGHDSLMWTALNHGGRTIFLEEDKSWIEQIKQKLPSL\n+--ESYHVVYDSKVHQADELMEVGMGE---DCK--V---VVDPRFSKCKL-\n+-SLKGFPNEVYDVEWDLIMVDAPTGYHDEAPGRMSAIYTAGLMARNRED-\n+-GETDVFVHDVDRVVEDKFSKAFLCEGYFREQE--GRIRHFTIPSHRTR-\n+S----GRSFCP-------\n+>3694.POPTR_0019s10490.1\n+--------------------------------------------------\n+--------------MRSKN----QSPINIKIIILGLFFLLFLLVIA-WSS\n+YSS-PRPNSSP-KA---ENDDLSDSSNL-STDE--EEPKP---------S\n+TAACPS-LPLTPTC--TKIPPSLANALVHYVTTNITPQQTLKEISVSLRV\n+LEKKSPCNFLVFGLGHDSLMWTSLNHGGRTVFLEEDKAWIEQIREKLPTL\n+--ESYHVTYDTRVHQADGLMETGMGD---ECK--V---VGDPRFSKCQL-\n+-ALKGFPGDIYDVEWDLIMVDAPTGYHDEAPGRMNAIYTAGLMARNREN-\n+-GVTDVFVHDVDRVVEDKFSKAFLCEGYMTEQE--GRLRHFIIPTHRTS-\n+S----GKPFCP-------\n+>3694.POPTR_0013s10240.1\n+--------------------------------------------------\n+--------------MRPNK---NQSPINIKIITLSLFFLLFLVLVA-WSS\n+FSS-PRSNPSP-KA---ENDDLTNPSSS-LSTDEEDQPKP---------S\n+TPACPS-LPLTPTC--TKTPPSLANALVHYVTTNITPQQTLKEISVTLRV\n+LEKKSPCNFLVFGLGHDSLMWTSLNHGGRTVFLEEDKAWIEQITEKLPSL\n+--EAYHVTYDTRVHQADGLMETGMGD---ECK--V---VSDPRFSKCQL-\n+-SLKGFPSDIYDMEWDLIMVDAPTGYHDEAPGRMTAIYTAGLMARNREN-\n+-GETDVFVHDVDRVVEDKFSKAFLCEGYLTEQE--GRLRHFIIPSHRTR-\n+S----GRPFCP-------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.069.AA.strNOG.ENOG411BE8B.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.069.AA.strNOG.ENOG411BE8B.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,470 @@\n+>88036.EFJ30497\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------EDFETDS-EEA--DASVS-EEE-DVSWISWFCGL\n+KGNEFFCEVDEEYIQDDFNLSGLCAQVPYYDYALDLILDVESPNEDILTE\n+EQNEMVESAAEMLYGLIHVRYILTSKGMAAMLEKYKKADFGRCPRFHCSG\n+QQCLPVGQSDIPRNGTVKMYCPKCEDLYYPRSKYQG---NI---------\n+-----------------D---GAY-------------------FGTTFAH\n+LLLMTNAYLKPAKPVQSYVPRIYGFKIHKS----A\n+>88036.EFJ23042\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------EDFETDS-EEA--DASVS-EEE-DVSWISWFCGL\n+KGNEFFCEVDEEYIQDDFNLSGLCAQVPYYDYALDLILDVESPNEDILTE\n+EQNEMVESAAEMLYGLIHVRYILTSKGMAAMLEKYKKADFGRCPRFHCSG\n+QQCLPVGQSDIPRNGTVKMYCPKCEDLYYPRSKYQG---NI---------\n+-----------------D---GAY-------------------FGTTFAH\n+LLLMTNAYLKPAKPVQSYVPRIYGFKIHKS----A\n+>88036.EFJ18690\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------EESDTES-EES--DVSGSDEGE-EFSWIPWYCAL\n+RGNEFFCEVDAEYIQDDFNLSGLSNQVPYYEYALDLILDVESPTDDMLTE\n+EQNEIVESAAEMLYGLIHVRYILTSKGMAAMLDKYKNVDFGRCPRVFCGG\n+QQCLPMGQSDIPRQSTVKIFCPKCEDIYYPRSKIQG---NL---------\n+-----------------D---GTY-------------------FGTTFPH\n+LFLMTYPHLKPARPTHTYVPKIYGFKIHKQRSSSK\n+>88036.EFJ36125\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------ESDTES-EES--DVSGSDEGE-EFSWIPWYCAL\n+RGNEFFCEVDAEYIQDDFNLSGLSNQVPYYEYALDLILDVESPTDDMLTE\n+EQNEIVESAAEMLYGLIHVRYILTSKGMAAMLDKYKNVDFGRCPRVFCGG\n+QQCLPMGQSDIPRQSTVKIFCPKCEDIYYPRSKIQG---NL---------\n+-----------------D---GTY-------------------FGTTFPH\n+LFLMTYPHLKPARPTHTYVPKIYGFKIHK------\n+>3218.PP1S15_279V6.1\n+---------------------------------------------MYKER\n+S--------AVLVREER-----GYRDNMKRLDDGIEKS------------\n+SASTSKGWI----GKEKDRLAPAAAATQ-----IRRY--------AGQEA\n+-RPTLDKMKYPDDVVAEDLESES-EES--DVSGS-DGE-DTAWISWFCGL\n+RGNEFFCEIDDEYIQDDFNLSGLRSQVPYYDYALDLILDVEPPSDDILTE\n+EQNELVESAAEMLYGLIHVRYILTSKGMNAMLEKCKNVDFGRCPRVHCSG\n+QPCLPMGQSDVPRTILVKIYCPKCEDIYYPRSKYQG---NI---------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYPHIKPSKPTQTYTPKVFGFKLHKSAR---\n+>3218.PP1S169_125V6.1\n+---------------------------------------------MYKDR\n+SSSLATEARGGNVRGELY---RDVTDNKKRFEGGIPLLQ-----------\n+PPSTSKGLI----GREKDRIAAAASKTQ-----TSRN--------AALEA\n+-RPTLEKAKYPEDVAAEDSESES-EDS--DVSAS-DGE-DTSWISWFCGL\n+RGNEFFCEVDDEYIQDDFNLSGLSSQVPYYDYALDLILDVESPSDDMLTE\n+EQNELVESAAEMLYGLIHVRYILTSKGMNAMLEKCKNVDFGRCPRVYCSG\n+QPCLPMGQSDVPRTSTVKIYCPKCEDIYYPRSKYQG---NI---------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYPYIKPSKPTQSYTPRIFGFKLHKSAR---\n+>3218.PP1S177_12V6.1\n+---------------------------------------------MYKER\n+SSSLPSEARGGNVRNEQQ-LYRDVTDNKKRLEDGIDKS------------\n+SPSTSRGGI----GREKDRIAAPAATTQ-----SRRN--------AGHET\n+-RPTMEKAKYPEDA--EDSESES-EDS--DVSAS-DGE-DTSWISWFCSL\n+RGNEFFCEVDDEYIQDDFNLSGLSSQVPYYDYALDLILDVESPSDDMLTE\n+EQNELVESAAEMLYGLIHVRYILTGKGMNAMLEKFKNVDFGRCPRVYCSG\n+QPCLPMGQSDVSRTSTVKIYCPKCEDIYYPRSKYQG---NI---------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYPYIKPSKPTQNYTPRIFGFKLHKSAR---\n+>4513.MLOC_53540.1\n+---------------------------------------------MQRDR\n+GVS-----------AAA-----GGAGERKRIGEAMDRS------------\n+SPSTSWGFS---GGRERDRIAAGKQPEV-----PRS-----------GGG\n+-STAMSKGKLSD----GESDTDS-EES--DLSGS-DGE-DTSWISWFCSL\n+RGNEFFCEVDDDYIQDDFNLCGLSGQVPYYEYALDLILDVESSHGDMFTE\n+EQNELIESAAEMLYGLIHVRYILTSKGLAAMLDKYKNYDFGRCPRVHCSG\n+QPCLPVGQSDIPRSSNVKIYCPKCEDLYYPRSKYQS---NI---------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYPHLKPQKPSQQYVPKVFGFKLHKP-----\n+>15368.BRADI5G17260.1\n+---------------------------------------------MHRDR\n+GVS-----------AAA-----GGAGERKRVGEAMDRS------------\n+SPSTSWGFS---GGRERDRIAAGKQPEM-----PRS-----------GGG\n+-STAMSKSKLSD----GESDTD'..b'MLYGLIHVRYILTSKGMAAMLEKFKNYDFGRCPRVYCCG\n+QPCLPVGQSDIPRSSTVKIYCPKCEDIFYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYGHLKPQKPSQRYVPRVFGYKIHKP-----\n+>4641.GSMUA_Achr4P30080_001\n+---------------------------------------------MSRER\n+GGSGS-------K----A-E--IGAVDRKRINDVLDKHLEKS--------\n+PPSASRGLN----SKEKDRMLVPSTSSG-----KQPE-------------\n+-PRSLLKS----KCSDEESETDS--E-ESDVSGSD-ME-DTSWISWFCNL\n+RGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDTFTE\n+EQNELVESAAEMLYGLIHVRYILTSKGMAAMLEKFKNYDFGRCPRVYCCG\n+QPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYGHLKPQKPSQRYVPRVFGFKLHKP-----\n+>4641.GSMUA_Achr2P10400_001\n+MESIEFANPDRRRGFRLVPLRKGAVNLFRARFGGDGRVDRREEGDMYRER\n+GGSGL-------K----V-E--IGAVDRKRINDALDKHMEKS--------\n+PPSASRGLN----SKEKDRLSVPSTSSG-----KQPE-------------\n+-HRSLSKN----KCSDEESETDS--E-ESDVSGSD-ME-DTSWISWFCNL\n+RGNEFFCEVDEEYIQDDFNLCGLSSQVPYYDYALDLILDVESSNGDMFTE\n+EQNELVESAAEMLYGLIHVRYILTSRGMAAMLEKFKNYDFGRCPRVYCSG\n+QPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYGHLKPQKPSQQYVPRVFGFKVHKP-----\n+>4555.Si030672m\n+---------------------------------------------MYKQG\n+G----------------------AGLDRKRISDALDKHLEKAVA------\n+SPSTSRGSAGGGGGRDHHRLVVPSSA------------------------\n+--SSMPKG----RCSEGESDSDS-E--ASDVSGSD-GE-DTSWISWYCNL\n+RGNEFFCEVDDDYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDMFTE\n+EQNELVESAAEMLYGLIHARYILTSKGLAAMLEKYKNYDFGRCPRVYCCG\n+QPCLPVGQSDIHRSSTVKIYCPKCEDIYYPRSKYQG---S--ILTILLLD\n+YLINACVCCPPKKCVSNS---NLF-------------------VRTQTKG\n+HFVLNLTLRMGCKCSHMHQRPFTHSSMSKH----H\n+>15368.BRADI1G27050.1\n+---------------------------------------------MYKQG\n+SAG--------------------AGLDRKRISDALDKHLEKAV---ASAA\n+SPSTSRGSAGAR--GDHNRLVVPSST------------------------\n+--SSIPKG----RCSEGESESDS-E--ASDVSGSD-GE-DTSWISWYCNL\n+RGNEFFCEVDDDYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDIFTE\n+EQNELVESAAEMLYGLIHARYILTSKGLAAMLEKYKNYDFGRCPRVYCCG\n+QPCLPVGQSDIHRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYDHLKPQKPSQRYAPRVFGFKLHKP-----\n+>39947.LOC_Os07g31280.1\n+---------------------------------------------MYKQG\n+GGGGG-------G----GGGGGGAGLDRKRISDALDKHLEKAVAAAAAAA\n+SPSTSRGSAGGRGGGDHQRLVVPSSA------------------------\n+--SSMPKG----RCSEGESESDS-E--ASDVSGSD-GE-DHSWISWYCSL\n+RGNEFFCEVDDDYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDMFTE\n+EQNELVESAAEMLYGLIHARYILTSKGLAAMLEKYKNYDFGRCPRVYCCG\n+QPCLPVGQSDIHRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYEHLKPQKPSQRYVPRVFGFKLHKP-----\n+>39946.BGIOSGA025742-PA\n+---------------------------------------------MYKQG\n+GGGG-------------GGGGGGAGLDRKRISDALDKHLEKAVAAAAAAA\n+SPSTSRGSAGGRGGGDHQRLVVPSSA------------------------\n+--SSMPKG----RCSEGESESDS-E--ASDVSGSD-GE-DHSWISWYCSL\n+RGNEFFCEVDDDYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDMFTE\n+EQNELVESAAEMLYGLIHARYILTSKGLAAMLEKYKNYDFGRCPRVYCCG\n+QPCLPVGQSDIHRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYEHLKPQKPSQRYVPRVFGFKLHKP-----\n+>4558.Sb02g033960.1\n+---------------------------------------------MYKQG\n+GAGG------------------GAGLDRKRISDALDKHLEKAVA------\n+SPSTSRGSAGGGGGRDHHRLVVPSSV------------------------\n+--STILKG----HCSEGESDSDS-E--ASDVSGSD-GE-DTSWISWYCNL\n+RGNEFFCEVDDDYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDMFTE\n+EQNELVESAAEMLYGLIHARYILTSKGLAAMLEKYKNYDFGRCPRVYCCG\n+QPCLPVGQSDIHRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYEHLKPQKPSQRYVPRVFGFKLHKP-----\n+>4577.GRMZM2G161611_P01\n+---------------------------------------------MYKQG\n+GAGG------------------GAGLDRKRINDALDKHLEKAVA------\n+SPSTSRGSA--GGGRDHHRLVVPSSV------------------------\n+--SSIPKG----RCSEGESDSDS-E--ASDVSGSD-GE-DTSWISWYCNL\n+RGNEFFCEVDDDYIQDDFNLCGLSSQVPYYDYALDLILDIESSHGDMFTE\n+EQNELVESAAEMLYGLIHARYILTSKGLAAMLEKYKNYDFGRCPRVYCCG\n+QPCLPVGQSDIHRSSTVKIYCPKCEDIYYPRSKYQG---N--I-------\n+-----------------D---GAY-------------------FGTTFPH\n+LFLMTYEHLKPQKLSQRYVPRVFGFKLHKP-----\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.070.AA.strNOG.ENOG411BEUV.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.070.AA.strNOG.ENOG411BEUV.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1254 @@\n+>3711.Bra036512.1-P\n+MGLCYSRN-----TSSVKDDE--IPVEQP--S---------------QT-\n+-----PRR------AS---------IPQSPIPS------------E---V\n+NSY-A------SSPFQS-----PLPAGV----------------------\n+A-----PS--PA--RTP-GR-KFKWPFPPPSPAKPIMAALRRRRGAPP-R\n+PRDE-PIPEDSE--DVD-------------GVG--GE-RLDKNFGFGKNM\n+EGKYELGKEVGRGHFGHTCWAKAKKGKMKGQTVAVKIISKAK--------\n+------------------------------------MTSALSIEDVRREV\n+KLLKALSGHKHMVKFYDVYEDNDNVYVVMELCEGGELLDRILA-------\n+------------RGGKYPEVDAKRILVQILSATAFFHLQGVVHRDLKPE-\n+------------------------------NFLFTSRNEDAVLKVIDFGL\n+SDFIRYD-------------------------------QRLNDVVGSAYY\n+VAPEVLHRSYSTEADMWSIGVISYILLCGSRPFYGRTESAIFRCVLRANP\n+NFEDMPWPSISPTGKDFVKRLLNKDHRKRMTAAQALAHPWLRD-ENPGLL\n+LDFSVYKLVRSYIRASPFRRSALKALAKAIPDEELVFLKAQFMLLDP-KD\n+GGLSLNNFTTALTRYATDAMMESKLPDILNTMQPLVQKKLDFEEFCAAGV\n+SVYQLEALEEWEQIATSAFEHFEQEGNRVISVQELAGEMSVGPN--AYPL\n+LKDWIRSSDGKLSFLGYAKFLHGVTVRSSSSRPR----------------\n+--------------------------------------\n+>59689.scaffold_602539.1\n+MGHCYSRNI-SAVEDD----E--IPTGND--EVSN---------QPSQS-\n+-----TEN------HR----HAS--IPQSPV-A-----------SGASEV\n+NSY-N------ISPFQS-----PLPAGV----------------------\n+A-----PS--PA--RTP-GR-KFKWPFPPPSPAKPIMAALRRRRGAPP-Q\n+PRDE-PIPEDSEDVADHGG-----------GGG--GE-RLDKNFGFGKNF\n+EGKYELGKEVGRGHFGHTCWAKAKKGKMKNQTVAVKIISKAK--------\n+------------------------------------MTSTLSIEDVRREV\n+KLLKALSGHRHMVKFYDVYEDADNVFVVMELCEGGELLDRILA-------\n+------------RGGRYPEVDAKRILVQILSATAFFHLQGVVHRDLKPE-\n+------------------------------NFLFTSRNEDAILKVIDFGL\n+SDFIRYD-------------------------------QRLNDVVGSAYY\n+VAPEVLHRSYSTEADMWSIGVISYILLCGSRPFYGRTESAIFRCVLRANP\n+NFEDMPWPSISPTAKDFVKRLLNKDHRKRMTAAQALAHPWLRD-ENPGLL\n+LDFSVYKLVKSYIRASPFRRSALKALSKAIPDEELVFLKAQFMLLDP-KD\n+GGLSLNCFTTALTRYATDAMMESRLPDILNTMQPLAQKKLDFDEFCAAAV\n+SVYQLEALEEWEQIATSAFEHFEHEGNRIISVQELAGEMSLGPS--AYPL\n+LKDWIRNSDGKLSFLGYAKFLHGVTVRSSSTRPR----------------\n+--------------------------------------\n+>3702.AT5G24430.1\n+MGHCYSRNI-SAVEDD----E--IPTGNG--EVSN---------QPSQN-\n+-----HRH------AS---------IPQSPV-A-----------SGTPEV\n+NSY-N------ISPFQS-----PLPAGV----------------------\n+A-----PS--PA--RTP-GR-KFKWPFPPPSPAKPIMAALRRRRGAPP-Q\n+PRDE-PIPEDSEDVVDHGG----------DSGG--GE-RLDKNFGFGKNF\n+EGKYELGKEVGRGHFGHTCWAKAKKGKMKNQTVAVKIISKAK--------\n+------------------------------------MTSTLSIEDVRREV\n+KLLKALSGHRHMVKFYDVYEDADNVFVVMELCEGGELLDRILA-------\n+------------RGGRYPEVDAKRILVQILSATAFFHLQGVVHRDLKPE-\n+------------------------------NFLFTSRNEDAILKVIDFGL\n+SDFIRYD-------------------------------QRLNDVVGSAYY\n+VAPEVLHRSYSTEADMWSIGVISYILLCGSRPFYGRTESAIFRCVLRANP\n+NFEDMPWPSISPTAKDFVKRLLNKDHRKRMTAAQALAHPWLRD-ENPGLL\n+LDFSVYKLVKSYIRASPFRRSALKALSKAIPDEELVFLKAQFMLLDP-KD\n+GGLSLNCFTMALTRYATDAMMESRLPDILNTMQPLAQKKLDFEEFCAAAV\n+SVYQLEALEEWEQIATSAFEHFEHEGNRIISVQELAGEMSVGPS--AYPL\n+LKDWIRSSDGKLSFLGYAKFLHGVTVRSSSSRPR----------------\n+--------------------------------------\n+>3702.AT3G49370.1\n+MGHCYSRNI-STV----DDDD-EIPSATA--QLPH---------RSHQN-\n+-----H-H------------Q-TSSSSSIPQ-S-----------PATSEV\n+NPY-N------ISPFQS-----PLPAGV----------------------\n+A-----PS--PA--RTP-GR-KFKWPFPPPSPAKPIMAALRRRRGTAP-H\n+PRDG-PIPEDSEA-----G-------GS-GGGI--GE-RLDKNFGFAKNF\n+EGKYELGREVGRGHFGHTCWAKAKKGKIKGQTVAVKIISKSK--------\n+------------------------------------MTSALSIEDVRREV\n+KLLKALSGHSHMVKFYDVFEDSDNVFVVMELCEGGELLDSILA-------\n+------------RGGRYPEAEAKRILVQILSATAFFHLQGVVHRDLKPE-\n+------------------------------NFLFTSKNEDAVLKVIDFGL\n+SDYARFD-------------------------------QRLNDVVGSAYY\n+VAPEVLHRSYSTEADIWSIGVISYILLCGSRPFYGRTESAIFRCVLRANP\n+NFDDLPWPSISPIAKDFVKRLLNKDHRKRMTAAQALAHPWLRD-ENPGLL\n+LDFSIYKLVKSYIRASPFRRAALKSLSKAIPEEELVFLKAQFMLLEP-ED\n+GGLHLHNFTTALTRYATDAMIESRLPDILNMMQPLAHKKLDFEEFCAASV\n+SVYQLEALEEWEQIATVAFEHFESEGSRAISVQELAEEMSLGPN--AYPL\n+LKDWIRSLDGKLNFLGYAKFLHGVTVRSSSSRPMR---------------\n+--------------------------------------\n+>59689.fgenesh2_kg.5__1288__AT3G49370.1\n+MGHCYSRNI-STV----DDDD-DIPSGIA--QLPH---------RSDQN-\n+-----H-H------------Q---SSSSIPQ-S-----------PATSEV\n+NPY-T------ISPFQS-----PLPAGV----------------------\n+A'..b'H\n+GSINLENIKMALMKNVTDQMKELHVQDILVSLGALQYRRMDFDEFCAATL\n+SVHQLEGLDRWEQHARCAYELFEKDGNRAIVIEELASELGLSPSVPVHVV\n+LRDWIRHTDGKLSFLGFVKLLHGVSSRSAQSLAKAR--------------\n+--------------------------------------\n+>4641.GSMUA_Achr1P21380_001\n+MGICYGKLA-SPE----NHDPSLSPT-PK--KKEE----V-S--TKK---\n+--------EGE-----GEPGV---T--------V--------AEERTSKP\n+WTS-P---F---FPFYS-----PSPAHSLFSKKS---PSVA-----SEG-\n+G-------GS--ATATP-RR-FFKRPFPPPSPAKHIRALLARRHGSVK--\n+PNEA-AIPEDEGE----E-----------G-RA--V-AGLDKSFGFSKGF\n+TSKYEIGEEVGRGHFGYTCTAKLKKGESNGQQVAVKVIPKAK--------\n+------------------------------------MTTAIAIEDVRREV\n+KILRALTGHNNLVHFYDAYEDNDNVYIIMELCEGGELLDRILS-------\n+------------RGGKYSEDDAKAVMVQILNVVAFCHLQGVVHRDLKPE-\n+------------------------------NFLFTSKDENSQLKAIDFGL\n+SDFVKPD-------------------------------ERLNDIVGSAYY\n+VAPEVLHRSYSTEADVWSIGVIAYILLCGSRPFWARTESGIFRAVLKADP\n+SFTELPWPSLSPEAKDFVKRLLSKDPRRRMTASQALCHPWTRNYNDIKVP\n+LDILIFRLIKAYLRSSSLRKAALRALSKTLTVDELFYLKGQFSLLEPNKN\n+GCITLENIKLALMKNATDAMKESRVQEFLLSLSALQYRRMDFDEFCAATL\n+SVHQLEGLDRWEQHARCAYELFEKDGNRAIVIEELASELGLGPSVPVHAV\n+LHDWIRHTDGKLSFLGFVKLLHGVSSRSVQSLAKAR--------------\n+--------------------------------------\n+>29760.VIT_03s0063g00940.t01\n+MGICASKPP-KQN----PYAPESLEP-SA--TP----G-A-V-SKDE---\n+--------A-------------------------------------EGPG\n+KRS-P---F---FPFYS-----PSPAHYLFSKK-----------S--P-A\n+V-------RS--ASSTP-RR-FFKRPFPPPSPAKHIKAVLARRQGK----\n+-KAA-AIPEGEGEE---------------EEAA--A-GGLDKSFGFSKQF\n+TSKYEVGEEVGRGHFGYTCSARFKKGERKGQQVAVKVIPKAK--------\n+------------------------------------MTTAIAIEDVRREV\n+KILRALTGHKNLVQFYDAFEDHDNVYIVMELCEGGELLDRILS-------\n+------------RGGKYSEDDARAVMVQILNVVSFFHLQGVVHRDLKPE-\n+------------------------------NFLFTSKDENSELKAIDFGL\n+SDFVKP-------------------------------DERLNDIVGSAYY\n+VSPEVLHRSYSTEADVWSIGVIAYILLCGSRPFWARTESGIFRAVLKADP\n+SFDEVPWPSLSSEAKDFVKCLLNKDPRKRITAAQALSHPWIRGYNGVKVP\n+LDILIFKLMKAYMRSSSLRKAALRALSKTLTVDELLYLKEQFAHLEPNKN\n+GTITLENIRTALMKNATDAMKESRIPDFLASLNALQYRRMDFEEFCAAAL\n+SVHQLEALDRWEQHARCAYELFDKDGNRAIMIEELASELGLGPSVPVHAV\n+LHDWIRHTDGKLSFLGFVKLLHGVSSRALAKAQ-----------------\n+--------------------------------------\n+>3847.GLYMA02G15220.1\n+MGVCTSKPQ-KPN----PYALREAEA-EA--DPSQNPK-T-T-LSPA---\n+--------G---------ADT---P--------R--------RKDDVSTG\n+KRS-P---F---FPFYS-----PSPARFLKKSP-----AP----A--G-G\n+S-------RS--ASSTP-RR-FFRRPFPPPSPAKHIRAVLARRQGKKA--\n+SATA-AIPEEG-------------------EEG--A-ADLDKRFGFSKEF\n+TSRLEVGEEVGRGHFGYTCSARFKKGELKGQQVAVKVIPKAK--------\n+------------------------------------MTTAIAIEDVRREV\n+KILRALNGHNNLIQFYDAFEDQDNVYIVMELCEGGELLDMILS-------\n+------------RGGKYSEDDAKAVMVQILNVVAFCHLQGVVHRDLKPE-\n+------------------------------NFLYAKKDESSELKAIDFGL\n+SDFVRP-------------------------------DERLNDIVGSAYY\n+VAPEVLHRSYGTEADVWSIGVIAYILLCGSRPFWARTESGIFRAVLKADP\n+SFDETPWPSLSLEAKDFVKRILNKDPRKRISAAQALSHPWIRNCNNVKVP\n+LDILIFKLMKTYMRSSSLRKAALRALSKTLTADELYYLRGQFALLEPSKN\n+GSISLENVNKALMKYATDAMKESRIPDFLSSLNSLQYRRMDFEEFCAAAL\n+SVHQLEALDRWEQHARCAYELFDKDGNRAIVIEELASELGLGPSIPVHVV\n+LHDWIRHTDGKLSFLGFVKLLHGVSSRSLAKVQ-----------------\n+--------------------------------------\n+>3847.GLYMA07G33260.1\n+MGVCTSKPQ-KPS----PYALREAEA-EA--DPSQIPK-T-P-LSPA---\n+--------A---------ADT---P--------R--------RKDDAITG\n+KRS-P---F---YPFYS-----PSPARFLKKSP-----AP----A--G-G\n+S-------RS--ASSTP-RR-FFRRPFPPPSPAKHIRAVLARRQGKKA--\n+SATA-AIPEEG-------------------EEG--A-ADLDKRFGFSKEF\n+TSRLEVGEEVGRGHFGYTCSAKFKKGELKGQQVAVKVIPKAK--------\n+------------------------------------MTTAIAIEDVRREV\n+KILRALNGHSNLIQFYDAFEDQDNVYIVMELCEGGELLDMILS-------\n+------------RGGKYSEDDAKAVMVQILNVVAFCHLQGVVHRDLKPE-\n+------------------------------NFLYAKKDESSELKAIDFGL\n+SDFVRP-------------------------------DERLNDIVGSAYY\n+VAPEVLHRSYSTEADVWSIGVIAYILLCGSRPFWARTESGIFRAVLKADP\n+SFDETPWPSLSLEAKDFVKRLLNKDPRKRISAAQALSHPWIRNYNNVKVP\n+LDILIFKLMKTYMRSSSLRKAALRALSKTLTADELYYLREQFALLEPSKN\n+GSISLENVNKALMKYATDAMKESRILDFLSSLNSLQYRRMDFEEFCAAAL\n+SVHQLEALDRWEQHARCAYELFDKDGNRAIVIEELASELGLGPSIPVHVV\n+LHDWIRHTDGKLSFLGFVKLLHGVSSRSLAKVQ-----------------\n+--------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1125 @@\n+>4533.OB08G22150.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------MYVTRPISRYENN\n+PQAA--AG-PPPEGPGSGILVVEGDEAV----ERAANC--WGLC--RDSE\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----V-RGLPLAQSRMAKVERTTEYLIAGDDDI----------------\n+--S-SEAF----VESDDVVFVPVIGLPLSSNRYYVVRAEGKHIGMVSACS\n+KEEDKTTFC-F--YS-RPKDVPARPFDHGDVYQQVELVQLK----GGKGF\n+RAEAVAADGIPPKYLRRKGWTIRTSSSTRYDNL-TDSARGVD-WPLRRRM\n+PDLSG-FGAGAKSSPPVVVGRWYCPFMFVRDG-R-RLKDQVRRCMFYEMT\n+LEQSWEEIYSRDN-V-HQ-GG-------GGGTVSA-TVRRST--ALLGGA\n+D--AVQGG--G--PQAVD-GVLWFRPASS----RSASAELGLDMVLWERM\n+KWELEKGG--WVAAAGDGE-TKRIERVER--RGG---RDRWDRFSCYLLV\n+ERFVLRRTDGSVALTYDFRHTD-KIRTLWS------\n+>39947.LOC_Os08g31910.1\n+MAHAPRVHMSEDKVCSMAHAPDTRTCPSQEWTFLAWGRSWTWPRMDVPGL\n+GLIDAAKSGHSWPGDVPGLGLIDGVDIRLGLIDVAKSGRSWPGDVPGLGL\n+IDGVDVPGLGLIDAVDVPGLGLIDAFTNINMIMGNVRMTYIVKQRKYVRE\n+DGEADRWMHGRGGSVEVCFQGRRMRAASDRGLDALPIDLEVGVPWCPPIG\n+AGWETGIYSRFVTGTYTDFCSSGGRAAAEGSGSWFLVMEDEAALERATVC\n+CGLCHGSGTHRHTCSASPFRRTGNSWWMERYMRGSKKMYVTRPLSRYLDN\n+PEAA--AE-PLPEGPGSGFLIVEDEAAV----ERATVC--CGLC--RDPK\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----V-HTLPFPQSRRLDVGE----------------------------\n+--------------DDIVLFVPVVGEPLSAGRYYVVKAIGHHAGKVLACS\n+REEDKTRIL-F--FS-FVDDAPPRPFHHGDIYQQVEVVAVAQASHWLRGF\n+KAVAVAPDGIPPSLLRRKGWEVSKAMRTSYDGL-NDDAHGID-WPLRRQM\n+PDLDG-FGIGAGGSPATVVGKWYCPFMFIRDG-EQRLKDQVKRCRFYEMT\n+LEQSWEEIYRCDN-T-HR-GSISG-KPPDEIKVNV-TVRRST--ALLGGT\n+GA-VVQEG--G--PQVVD-GVMWFRPAAPPT-NSGVAGGVGLDMVVWEKM\n+KWELERGG--WVAGNGD---VESIERVERG-EAA----GQWDKFGCYLLL\n+ESFVLRRMDGSVALTCGFRHTS-KITTKWV------\n+>39947.LOC_Os08g31880.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------------MSRYQDD\n+PDAA--AE-PPPEDPGSGFLVVEDEVAV----ARATRW--WGLW--ADRQ\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----V-YGLPFPQSRQLEVEYTASIGAGRNR------------------\n+---------LTYTHRDDVVFVPVVGQPLSSGRYYAARATGRHAGKVSACS\n+REEDMVTCCGL--WS-LVNDVPPRPFDRGDVYQQVEVLRLPP---RGRGF\n+TAVAVAPDGIPPGYLRREAWKVHTSASTSYD-L-ADAAHGTD-WPLRRRM\n+PDLDS-FDVGVGGSPPVVVGRWYCPFMFINDGGEQRLKDQVKRCMFYEMT\n+LEQRWEEIYTRDN-A-HR-GRRSTSSKDNEVEVSA-TVRRST--ALLGGT\n+D--AVRGG--G--PQMVD-GVMWFRPAAPPT-NSGTAGGVGLDMVVWEKM\n+KWELERGG--WVAGNGD---VESIERGERR-EAR---PGQWDKFGCYLLL\n+ESFVLRRMDGSVALTCGFRHTG-KIRTKWV------\n+>39947.LOC_Os08g31890.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------'..b'-LRDQMKRSMFYEIS\n+LEQFWQKVYACEN-H-SG-HDK-------VVEVNA-LFGSLL--VMMDGG\n+KE-VVQDR--T-V-HGDD-GMVWFKPLD---S---RAKGIGLSLAMWESI\n+KWEQGRGG--WIADE-----EERMVRLEQY----EG-MNRWKKFACYVLV\n+ERFVVKRIDGSLVLTFDFRHSI-KVRSKWD------\n+>4641.GSMUA_Achr3P06220_001\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------MYVTRPLSTFKNA\n+AGA--VHQ-PPLEGPGSGYLLLQDEELQ----PASTCC--WGACKCDPDR\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----I-QQLPFPQNKILTLSYSEQRG-----------------------\n+--------ETTDTYGSAALFIPVPNQPLSTNRYYVITAKGKHKGKAYTCS\n+KEEDMTSCCV-C--Q-CINDVKPKEFDHRDVYQQMEIVCYK------GRF\n+TARPVASDAIPPSILRKEYWRLHQVEHEEYA-L--GVAAGLD-EALRSRL\n+PELH---------AAGVVVGRWYTPFVFVKEEM-D-LRDQVKHSAFYEVT\n+LEQFWEEVYACEN-R-HG-AEK-------VAEVKA-VVRGEA--AFLDGK\n+E--AKRY---D-T-HDVD-GLVWFKPLD---S---GGGAVKLSFPVWERM\n+KWEQSRWG--WTGDE-----EQKVEKIVEY----GG-EGGWKSLRCYVLV\n+ERFAVRRMDGSLVLMVDFRHSSHKVKCIWE------\n+>4641.GSMUA_Achr5P27360_001\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------MYTTRPLSVFKNS\n+AGAAAIQP-PPPAGPNSGYLLLQDEGAE----PNPSCC--WGLC--EDTR\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----V-RELPFPQNRILTITYTEGT------------------------\n+-----------HTWQLPALFIPVLDKSLSSNHYYVIVAKGKKKGKAYTCS\n+LEEDMTTCCF-C--R-SVNDVKPREFDHRDIYQQVEIVCKR------GRF\n+TAQSVAPDGFAPWPLRSKYWELYASKPTDFD-L--TDAWGLD-KALRART\n+PALE--LPISGAGGAGLVVGRWYAPCVFVKEGD-S-LRRQMERSAFYDIT\n+LEQRWEQVFACEN-L-YG-DRR-------TVEVKA-TVGAEG--AVLGGV\n+E--ATRD---G-A-GGQD-GVVWYKPLD---L---EGERVGLSSPVWERM\n+RWEQGRGG--WVGGE------VKVERSEEY----GG-VSPWKKFGCYVLV\n+ERFVVRRMDGSSALIVDFKHTG-TIQTKWE------\n+>4641.GSMUA_Achr5P27350_001\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------MYTTRPLSVFKNS\n+AGAAAIQP-PPPAGPNSGYLLLQDEGAE----PNPSCC--WGLC--EDTR\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----V-RELPFPQNRILTITYTEHNG-----------------------\n+--------QSSTTHRFPALFIPVLYKSFSSNHYYVIVAKGKKKGKAYTCS\n+LEEDMTTCCF-C--Q-CVNDVKPREFDHRDIYQQVEIVCKR------GRF\n+TAQSVAPDGFAPWPLRRKDWRLYASKPTDFD-L--TDAWGLD-KALRART\n+PALE--LPISGAGGAGLVVGRWYAPCVFVKEGD-S-LRRQMERSAFYDIT\n+LEQRWEQVFACEN-L-YG-DRR-------TVEVKA-TVRAEG--AVLGGV\n+E--ATRD---G-A-GGQD-GVVWFKPLD---L---EGERVGLSSPVWERM\n+RWEQGRGG--WVGGD------VKVERSEEY----GG-VGPWKRFGCYVLV\n+ERFVVSRMDGSSALIVDFKHTG-TIQTKWE------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.072.AA.strNOG.ENOG411BF1S.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.072.AA.strNOG.ENOG411BF1S.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,279 @@\n+>88036.EFJ04935\n+MDGV-------------------------------TGGDVELMSKSLQVE\n+HKLFYFDLKENPRGRYLKISEKTTTSRSTIIVPESGIVWFLDLFNLYSN-\n+-GD-DKFESKELQMDTK---------------------------VFYFDV\n+GENPRGRFLKISEVSAASVRSTIIVPSGNDADEGWVQFRHVLAEIH-EAS\n+QMLLSS------IE-NRQVSSQVLLKFQKSSPINAGFYDGPVRN----GP\n+TVA------PPSNDTSRMSSTARVLRAEQKKFFFDLGSNARGQYLRISEV\n+IGGDRSAIILPASALEQFHETVGEFVELLKAQEQQ-VSSAVLAD--PGYT\n+K---\n+>88036.EFJ20042\n+MDGV-------------------------------TGGDVELMSKSLQVE\n+HKLFYFDLKENPRGRYLKISEKTTTSRSTIIVPESGIVWFLDLFNLYSN-\n+-GD-DKFESKELQMDTK---------------------------VFYFDV\n+GENPRGRFLKISEVSAASVRSTIIVPSGNDADEGWVQFRHVLAEIH-EAS\n+QMLLSS------IE-NRQVSSQVLLKFQKSSPINAGFYDGPVRN----GP\n+TVA------PPSSDTSRMSSTARVLRAEQKKFFFDLGSNARGQYLRISEV\n+IGGDRSAIILPASALEQFHETVGEFVELLKAQEQQ-VSSAVLAD--PGYT\n+K---\n+>3218.PP1S26_202V6.1\n+MENA-------------------------------PGGDAELVCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSGSRSTIIVPVAGIVWFVDLFNYYAN-\n+-GE-EELSSKELQLDTK---------------------------VFYFDV\n+GENQRGRFLKVSEASVTRNRSTIIVPAGNAADEGWAAFRNILVEIH-EAS\n+QLLLPPTASSGPLQPVQQGTSSQEHMGVMSDNVGSGYLPSTSSPI-ASAS\n+TVPLPEVGSSNVGLAGGGLATARVIRAEQKKFFFDLGSNARGQYLRISEV\n+TGVDRSAIILPVAALAQFHETLGQFVEVVKSQGPIGPNVANGQRYAETET\n+II--\n+>3218.PP1S36_94V6.1\n+MEGA-------------------------------PGGDAELVCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSGSRSTIIVPVAGIVWFVDLFNYYAN-\n+-GE-EELSSKELQLDTK---------------------------VFYFDV\n+GENQRGRFLKVSEASVTRNRSTIIVPAGNAADEGWSSFRNILVEIH-EAS\n+QLLLPPSASSG---PLQQGGILQEHMGVMADNVGAGYLPSTSSPP-ASAS\n+TVPLPEVGSPNVASSGGGLATARVIRAEQKKFFFDLGSNARGQYLRISEV\n+TGVDRSAIILPVAALEQFHETLGQFVEMVKSQGPIGPNVVNVRTIAPPRK\n+RAES\n+>4081.Solyc01g049680.2.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------MQVSEASVSRNRSTIIVPAGSARDEGWAAFRNILAEIN-EAS\n+RLFISP---------NQQSLETSERL-GLSDDVGAGFISSHSSQS-APTA\n+DLTIERTIDLPAADEVSDVGVSKVIRVDQKRFFFDLGNNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFYDMVGHFVEISKDRLEG-ITGANVRT--IDSP\n+QR--\n+>3694.POPTR_0003s20690.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---MLP---------NQQSSETSERLVGLSDDVGAGFISGHSSQS-VTTS\n+ELNVDRSVELPPQDEIGNMAVSKVIRVDQKRFFFDLGSNNRGHFLRISEV\n+AGNDRSSIILPLSGLKQFHEIVGHFVEITKDRIEG-MTGANVRT--VDPP\n+QR--\n+>3694.POPTR_0001s03780.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---MLP---------NQQSSETSEQLVGLSDDVGAGFISGHSSQSPAPTS\n+ELNVDRSVDLPPQDEIGNLGVSKVIRVDQKRFFFDLGSNNRGHFLRISEV\n+AGNDRSSIILPLSGLKQFHEIVGHFVEITKDRIEG-MTGANIRT--IDPP\n+RR--\n+>4577.GRMZM2G049429_P01\n+MDGGGGG-GGG-GGGVGAGVMVGGGVVPGG-----GGGDVELVSKTLQFE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPIDGVAWFLDLFDYYIR-\n+-TDERDVFSKELRLQTK---------------------------VFYFDI\n+GENKRGRFLKVSEASVNRNRSTIIVPAGSSGEEGWEAFRNVLLEINNEAS\n+RLYVLP---NH---PNQQHMEPPERLPGLSDDVGAGFIAGHGSQS-ASGP\n+EVDVERLVDLPPQEEISGMGMSKVIRADQKRFFFDLGSNNRGHYLRISEV\n+AGVDRSSIILPLSGLKQFHEMVGHFVDIMKDRLEG-MTGANVRT--VESS\n+QR--\n+>15368.BRADI2G09470.1\n+MDGGGGVGGGM-AGPVGGGMVGPVGVGVGG--GGGGGSDVELVSKTLQFE\n+HKLFYFDLKENPRGRYLKISEKTSTTRSTIIVPIAGVAWFLDLFDYYIR-\n+-TDERDVFSKELRLDTK---------------------------VFYFDI\n+GENKRGRYLKVSEASVNRNRSTIIVPAGSSGEEGWEAFRNVLLEISDEAS\n+RLYVLP---NH---PSQQHLEPPERLPGLSDDVGAGFIAGHASQS-ASGP\n+EVDVERLVDVPPIEEFSGMGLSKVIRADQKRFFFDLGSNNRGHYLRISEV\n+AGADRSSIILPLSGLKQFHEMVGHFVDIMKDRLEG-MTGANVRT--VEPS\n+QR--\n+>4513.MLOC_51913.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------MGLSKVIRADQKRFFFDLGSNNRGHYLRISEV\n+AGADRSSIILPLSGLKQFHEMVGHFVDIMKDRLEG-MTGANVRT--VEPS\n+QR--\n+>4555.Si002339m\n+MDGGGG-GGGG-GGVVGGGVMVGGGVGPGGG-GVGGGGDV'..b'HFVEITKDRLGG-IPAVNVRT--LEPV\n+QR--\n+>3711.Bra005613.1-P\n+MEGNSGG-G----------AATV------G--GGGGGSDVELVSKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVN-\n+-SEEHELFSKELQLDSK---------------------------VFYFDI\n+GDNRRGRFLKVSEASVSRNRSTIIVPAGSSPDEGWAAFRNILAEIH-EAS\n+GLFAMP---NQ------KPSDAQEHLVGLSDDVGAGFIPGHGNQPASSSS\n+ELTVERATDLPGQDEAGLTGISKVIRADQKRFFFDLGNNNRGHFLRISEV\n+AGSDRSSIILPLSGLRQFHEVIGHFVEITKDKIDG-MTGANVRT--IDPP\n+HR--\n+>3702.AT2G32080.1\n+MEANSGG-GG----GAEGGRAVTG----GG--GGGGGSDVELVSKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVN-\n+-SEEHELFSKELQLDSK---------------------------VFYFDI\n+GENRRGRFLKVSEASVSRNRSTIIVPAGSSPDEGWAAFRNILAEIH-EAS\n+GLFVMP---NQ-----VKPSDGQEHL---VDDVGAGFIPGHGSQQ-PSSS\n+EHNVDRTIDSPGQEETGMTGVSKVIRADQKRFFFDLGNNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFHEVIGHFVEITKDKIEG-MTGANVRT--VDPP\n+QR--\n+>59689.fgenesh1_pm.C_scaffold_103000004\n+MEANSGG-------GAEGGRAATG---------GGGGSDVELVSKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVN-\n+-SEEHELFSKELQLDSK---------------------------VFYFDI\n+GENRRGRFLKVSEASVSRNRSTIIVPAGSSPDEGWAAFRNILAEIH-EAS\n+GLFVMP---NK-----VKPSDGQEHL---VDDVGAGFIPGHGSQQ-PSSS\n+EHNVDRSVDSPGQEET----VSKVIRADQKRFFFDLGNNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFHEVIGHFVEITKDKIEG-MTGANVRT--VDPP\n+QR--\n+>59689.Al_scaffold_0004_1668\n+MEANSGG-------GAEGGRAATG---------GGGGSDVELVSKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVN-\n+-SEEHELFSKELQLDSK---------------------------VFYFDI\n+GENRRGRFLKVSEASVSRNRSTIIVPAGSSPDEGWAAFRNILAEIH-EAS\n+GLFVMP---NK-----VKPSDGQEHL---VDDVGAGFIPGHGSQQ-PSSS\n+EHNVDRSVDSPGQEET----VSKVIRADQKRFFFDLGNNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFHEVIGHFVEITKDKIEG-MTGANVRT--VDPP\n+QR--\n+>3694.POPTR_0001s03790.1\n+MEGNSGG-------GSGS--GAAA----AG--GGGGGNDVELMCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPFSGISWFLDLFNHYVDN\n+SADDQDLFSKELQLDTK---------------------------VFYFDI\n+GENRRGRFLKVH---CSPSKIYIIAP------------------------\n+--------------------------------------------------\n+------------------------------------------HIIK----\n+--------------------------------------------------\n+----\n+>3694.POPTR_0003s20700.1\n+MEGNSGG-VGGGGSGSGG--GGGG----GG--GGGGGNDVELMCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPFSGISWFLDLFNYYVNN\n+SADDQDLFSKELQLDTK---------------------------VFYFDI\n+GENRRGRFLKKS--------------------------------------\n+--------------------------------------------------\n+------------------------------------------TYLG----\n+--------------------------------------------------\n+----\n+>4081.Solyc01g049690.2.1\n+MEGNSSG-------------------------GGGGGNDVELLCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPFNGISWFLDLFNYYVN-\n+-SDDQDVFSKELQLDTK---------------------------VFYFDV\n+GENRRGRFLKLS--------------------------------------\n+--------------------------------------------------\n+------------------------------------------GLQL----\n+-----------------WVG------------------------------\n+----\n+>29760.VIT_06s0004g00040.t01\n+MEGNSG------------------------------GNDVELLCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPFSGISWFLDLFNYYVN-\n+-SDEQDVFSKELQLDTKAFLFLLLFLIFRPCFSIHHPMPILCFQVFYFDI\n+GENRRGRFLKVSEASVSRNRSTIIVPAGSTRDEGWAAFRNILAEIN-EAS\n+RLFILP---NQ------QSSEPSERLVGLSDDVGAGFISGHSTQP-APAS\n+ELNVERSVELPAQDEIGNLGVSKVIRADQKRFFFDLGSNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFHEMVGHFVEITKDRIEG-MTGANVRT--VDPP\n+QR--\n+>3847.GLYMA07G35160.1\n+MEGNSGG--------------------------GGGGNDVELLCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPFSGISWFLDLFNYYVN-\n+-SDDQDLFSKELQLDTK---------------------------VFYFDI\n+GENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNVLAEIN-EAS\n+RLFILP---NQ------QNSESSERLVGLSDDVGAGFISGHSTQP-ATSS\n+ELNVDRSVDLPPQDEIGNLGVSKVIRADQKRFFFDLGSNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFHEIVGHFVEITKDRIEG-MTVANVRT--VDPP\n+QR--\n+>3847.GLYMA20G03020.1\n+MEGNSGG---------------------GG--GGGGGNDVELLCKTLQVE\n+HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPFSGISWFLDLFNYYVN-\n+-SDDQDLFSKELQLDTK---------------------------VFYFDI\n+GENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEIN-EAS\n+RLFILP---NQ------QNSESSEHLVGLSDDVGAGFISGHSTQP-ATSS\n+ELNVDRSVDLPPQDEIGNLGVSKVIRADQKRFFFDLGSNNRGHFLRISEV\n+AGSDRSSIILPLSGLKQFHEIVGHFVEITKDRIEG-MAVANVRT--IDPP\n+QR--\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.073.AA.strNOG.ENOG411BFCW.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.073.AA.strNOG.ENOG411BFCW.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,49005 @@\n+>3694.POPTR_0107s00200.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------MTAVVHCLGIWRVYLLGPKFIVKTD\n+NVANTFFK------------------------------------------\n+'..b'-----------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------MIMGLDSVDIILGTDWLSRHHAVIDVAARAIEI\n+RSPLDGEITLYLPDQGCT------RSCAFV-MLESP------------VE\n+KIPVVCDYPDVFPDELPGMPPDRDIEFAIELQPGTAPISKRPYRMPPAEL\n+AELKKQLQELLDKGFICPSTSPWGCPALFVKKKDESLRMCVDYRPLNAVT\n+IKNKYPLPRIDVLFDQLVGAKVFSKIDLRSGYHQIKIRASDIPKTAFSTR\n+YGLYEFLVMSFGLTNAPAYFMYLMNSVFMPELDKFVVVFIDDILVYSKNE\n+AEHTEHLHIVLQRLRDHHLYAKLSKCEFWLKEIKFLGHTISQDGISVDPE\n+KVQEVMDWKPPTTVKQIQSFLGLAGYYRRFIPNFSRIAKPMTELLKKGVK\n+FEWSQKCEDAFHTLRQHLTTAPVLAQPDNTKPFEVYCDASGTGLGCVLMQ\n+ENRVIAYASRALRPHEQNYPTHDLELAAVVHALKLWRHYLMGAHCNIYTD\n+HKSLKYIF------------------------------------------\n+----TQADLNMRQRRWLELIKDYDLEVLYHPGKANVVADALSRKAQ--CN\n+CMNMDVGVTTLCDELCRLN-----LEV-VSSGDLSYISVEPTLQEQIVRA\n+QVEDKGVQIIKDMIKQKADKYKCFRQDSKGILWFGDRLVV--PKDPELRK\n+QILDEAHLSKFSMHPGSNKMYHDLRSLYWWTRMKREIAKYVSECDTCQRI\n+KASHLKVAG-----------------------------------------\n+-PLQPLPIPSWKWEGICMDFIVGLPNTSRHHDSIWVIVDRLTKTAHFLPV\n+HTTHKTEKYAEIYVDQIVRLHGIPKTIISDRGALFVARFWEKLQESLGTQ\n+VIRSSAYHPQTDGQTERVNQILEDMLRACALHYGKDWDKCLSLAEFSYNN\n+SYQSSLKMAPFEALYGRRCRT-P--LN--WSQAEEREIFGPDLVLEAEAK\n+V----------------KVITKNLEA------------------------\n+--------------------------------------------------\n+-----------------------------------------AQAR---QR\n+SYHDKRRKPLQF--------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.074.AA.strNOG.ENOG411BFPF.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.074.AA.strNOG.ENOG411BFPF.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,527 @@\n+>3711.Bra014654.1-P\n+M---C----ALVPPLFR----NFGWSLTGE-Y--E--S--YYGGGDHLTN\n+G-TI--------------FDFPETF--G-VVHQ---Q-N-RLWVSVS---\n+-----SEGIGI--DKNPVVTKKLKHNASERDRRKKINSLFSSLRSCLPAS\n+DQS----KKLSIPQTVSRSLKYIPELQEEVKKLIQKKEEFLV---RVSG-\n+-Q--RD-IE-HHVK--QQPKVVARYVSTVSVTRLGDNKVMVQISSSKI--\n+-H-SFSISNVLSGLEEDGFVLVDVSSPRS-HDERLFYTLHLQMGYI--DY\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KMN-----------C----------\n+--TELSQ---RILY--LYEE-CGNSF------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------R-----------R\n+>3711.Bra014658.1-P\n+M---C----ALVPPFFP----NFGWPSTGE-Y--E-SYYLSGENLDNCTF\n+F-D---------------FPVPETY--G-LVHQ---Q-N-SLGVSIS---\n+-----SAGIGI--DKSPVVNKKLKHNASERDRRKKINSLFSSLRSCLPAS\n+DQS----KKLSIPQTVSRSLKYILELQEEVKMLIQKKEELLV---RVSG-\n+-Q--RA-IE-------QQPKVVAHYVSTVSATRLGDHEMMVQISSSKI--\n+-N-NFSISNVLSGLEDDGCVLVDVSSSRS-QGERVFYTLHLQVDNID-ND\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KLN-----------C----------\n+--TELSQ---RMLY--LYEE-CGNSY------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------\n+>3711.Bra014657.1-P\n+M---C----ALVPPVFP----NFGWPSTGE-Y--E-SNYLVGENLDDFTF\n+L-D---------------CPAPETY--G-VEHHQEIQ-E-MLGVSVP---\n+-----SEG-------NGVVTKKLNHNASERDRRKKINSLFSSLRSCLPAS\n+DQS----KKLSIPQTVSRSLKYIPELQEQVKKLIQKKEELLV---RVSG-\n+-Q--RD-IE-HYVE--PHPKAVARYVSTISATKLGDNEVMVQISSSKN--\n+-H-NFSISNVLSGLEEDGFVLVDVSSSRS-HGERLFYTLHLQMGNKD-DY\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KLT-----------C----------\n+--EELRQ---RMLY--LYEE-CGNSF------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------R------------\n+>3711.Bra014659.1-P\n+M---C----ALVPPLFP----DFGWPSTAGYE--R-SYYLGGENLNNDMF\n+L-D---------------FPVLETY--G-VLAH--HQ-N-SLGVSVS---\n+-----SEGNGI--DNNPVVKKKLNHNASERDRRKKINSLFASLRSCLPTS\n+DQS----KKLSISATVSRSLKYIPELQEQVKKLLQKKEELLV---RVSG-\n+-Q--RD-IE-LYVK--PQPKTVASYVSTVSATRLGDNEVMVQISSSKI--\n+-N-NFSISNVLTGLEEDDFVLVDVSSSRS-QGERLFYTLHLQVENMDDHY\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KMN-----------C----------\n+--EELSE---RMLY--LYEE-CENSF------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------R------------\n+>59689.fgenesh2_kg.5__2132__AT3G56970.1\n+M---C----ALVPPLFP----NFGWPLTGQ-C--E-SYYGGGDNLNNGTF\n+L-D---------------FPVPPTY--G-VLTH--HQ-N-SLEVSVS---\n+-----SEGNEI--ANNPVVAKKLNHNASERDRRKKINSLFSSLRSCLPVS\n+DQS----KKLSIPETVSKSLKYIPELQQQVKKLLQKKEELLV---RVSG-\n+-H--RD-FE-IYDK--QQSKAVASYLSTVSATRLGDNEVMVQISSSKI--\n+-H-NFSISNVLGGIEEDGVVLVDVSSSRS-QGERLFYTLHLQVENMDDYY\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KIN-----------C----------\n+--EELSE---RMLY--LYEK-CENSF------------------------\n+--------------------------------------------------\n+-------------------------------'..b'TTVSRVLKYIPELQKQVDNLERRKKELTN---ANCK-\n+-P--GV-LK--------T--T-KAVTPIVSATCLNDTEIMVQVSLHSDVA\n+AT-ALPLSKCIKVLENEGLHLVSSSTYSSAFENKTFYSLHLQF-QA---P\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------NPQ-----------A----------\n+--RGVTG---SLSISR-IRERPQQ-T------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------K------------\n+>4555.Si002720m\n+---M--DHQLFDDP-FA----SS-ISSLE---------------------\n+----AD-IFSAGG----QLPSPPWPDLD-LDDD--DIHD-LSAPAANATS\n+S--GGYGSG-----GGSGSHRKLSHNAYERDRRKQLNELYSSLRSLLPDA\n+DHT----KKLSIPTTVSRVLKYIPELQKQVDNLERRKKELTN---ANCK-\n+-P--GV-LN--------A--S-EIITPIVSATCLNDTEIMVQVSLQSNMA\n+AT-TLPLSKCIKVLENEGLHLISSSTYS-TLDNKTFYSLHLQRSQR--TM\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KEE-----------C----------\n+--PGFCD---ELE--RIVRK-KAG--------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------A------------\n+>4558.Sb03g046090.1\n+---M--DHQLFDDP-FG----SS-ISSLE---------------------\n+----AD-IFSAGGGG--QLPSPPWPDLD-LDDD-YDIHD-LSAPAANAAT\n+SSGGGYGSG--------GSGRKLSHNAYERDRRKQLNELYSSLRSLLPDA\n+DHT----KKLSIPTTVSRVLKYIPELQKQVDNLERRKKELTN---ANCK-\n+-P--GV-LN--------T--K-EIVTPIVSATCLNDTEIMVQVSLHSNVA\n+AT-ALPLSKCIKVLENEGLLLVSSSTYS-TFENKTFYSLHLQRSQR--TM\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------KEQ-----------C----------\n+--PGFCD---ELE--KIVRK-KAG--------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------A------------\n+>4641.GSMUA_Achr8P22120_001\n+---------------------MG-WQPEDI-T--A-H---VLHYEDPFAC\n+Y-PYMEE-------------------LE-IGHD-DLLRH-CSVLAA----\n+----K--DD------SSSSTKKLCHNAYERDRRKKLNDLYSSLRDLLPES\n+DQARKKKKKLSIPLIVCRVLKYVPELQRQVERLSRRKEEILL---ALSR-\n+-P--EE-QS--------HCVRSAVQYPMVSATCLSKREVMVQLCVVNKDA\n+T---FSFSKILKVLEREGLHLMNSSNYTT-CDGRCVCSLHLQARED---F\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------RSE-----------C----------\n+--RIFCE---HLME--EIKE-QARHG------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------SN----LPRSLWM\n+>4641.GSMUA_AchrUn_randomP14860_001\n+---------------------MG-WPPEDM-A--A-Q---DLQCEDHFVC\n+C-TSKETDVSCQSL---GFSSRP-LERE-IVDQ-DELHY-YTLIAM----\n+--------D------SSSSTKKLCHNAYERGRRKKINDLYASLRALLPES\n+DQS----KNLSIPLTISRVLKYIPELQRQVERLQQRKEEILL---ALSR-\n+-P--EE-QS--------HCGDIVVYRPMVSAACLSNREVMVQVCLLSSHF\n+S---ISFSKILRLLKREGLHLVNASTYTT-HDGRCFCSLHIEARET---F\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------DTE-----------C----------\n+--RIFCD---TLLK--EIKE-QAELG------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------SR----ITWNM--\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.075.AA.strNOG.ENOG411BFQS.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.075.AA.strNOG.ENOG411BFQS.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,420 @@\n+>39946.BGIOSGA012379-PA\n+MGSSTDH----GGAGG---R-GKKG---S-G-S-QLWKKALLHSSLCFVM\n+GFFTGFAPSSVSDWTS----AA-----VSAG-GVGSSHVVRS---LH---\n+---------AT-G-GAAVNRSLLA-Q---AA---AGAV--------D-AG\n+----------------------------PQPLLVVVTTTESTPSAAGQRA\n+AALTRMAHTLRLVPPPLLWVVVEANPDV--AATARLLRTTGLMYRHLTYK\n+--DNFTVADAAAGKERHHQRNVALGHIEHHRLAGVVLFAGLGDTFDLRFF\n+DQLRQIR-TFGAWPVATMSQNERKVVVQGPACSSSSVAGWFSMDLSNATS\n+PVAVGGAGYGAAA-----ARPRELDVHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSVKFVQQVVLEDYSKVRGIPS-DCSEVMV----------------\n+----------------------------WHVNTTPLPSSQPSPQNKR---\n+--------------\n+>39947.LOC_Os03g17850.1\n+MGSSTDH----GGAGG---R-GKKG---S-G-S-QLWKKALLHSSLCFVM\n+GFFTGFAPSSVSDWTS----AA-----VSAG-GVGSSHVVRS---LH---\n+---------AT-G-GAAVNRSLLA-Q---AA---AGAV--------D-AG\n+----------------------------PQPLLVVVTTTESTPSAAGQRA\n+AALTRMAHTLRLVPPPLLWVVVEANPDV--AATARLLRTTGLMYRHLTYK\n+--DNFTVADAAAGKERHHQRNVALGHIEHHRLAGVVLFAGLGDTFDLRFF\n+DQLRQIR-TFGAWPVATMSQNERKVVVQGPACSSSSVAGWFSMDLSNATS\n+PVAVGGAGYGAAA-----ARPRELDVHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSVKFVQQVVLEDYSKVRGIPS-DCSEVMAKLRTVSQQLEATWRSA\n+LA---IINELLRACASVHGHVRSKLDSLYRSDFPQTEPETLICLIHDHAS\n+HYIYGGRFLSGDFC\n+>4538.ORGLA03G0128500.1\n+MGSSTDH----GGAGG---R-GKKG---S-G-S-QLWKKALLHSSLCFVM\n+GFFTGFAPSSVSDWTS----AA-----VSAG-GVGSSHVVRS---LH---\n+---------AT-G-GVAVNRSLLA-Q---AA---AGAV--------D-AG\n+----------------------------PQPLLVVVTTTESTPSAAGQRA\n+AALTRMAHTLRLVPPPVLWVVVEANPDV--AATARLLRTTGLMYRHLTYK\n+--DNFTAADAAAGKERHHQRNVALGHIEHHRLAGVVLFAGLGDTFDLRFF\n+DQLRQIR-TFGAWPVATMSQNERKVVVQGPACSSSSVAGWFSMDLSNATS\n+PVAVGGAGYGAAA-----ARPRELDVHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSVKFVQQVVLEDYSKVRGIPS-DCSEVM-----------------\n+-----VCNELLRACASVHGHVRSKLDSLYRSDFPQTEPETLICLIHDHAS\n+HYIYGGRFLSGDFC\n+>4577.GRMZM2G118959_P01\n+MGSSTDH----GGAGW---R-GKKQ-----G-S-QLWKKALLHSSLCFVM\n+GFFTGFAPSSVSDWTS----AA-----AAAGSSSSSSHVVRA---LP---\n+---------A----GGALNRSLLA-H---GA---GPGY------DRAAS-\n+----------------------------PRPLLVVVTTTESTPVASGERA\n+AALTRTAHALRLVAPPLLWVVVEAAPDA--PATARQLRATGLMYRHLTYR\n+--DNFTAA--GAGKERHHQRNVALGHVEHHRLAGVVLFAGLDDVLDLRLF\n+DQIREIS-AFGAWPVATMWRDEREVVVRGPACSSSAVTGWFSQDLSDGTA\n+AAA---STTSTAR----ARPSGEVDVHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSTKFVQQVVLEDLSKVKGIPS-DCSEVMVWHVDTAAPSPSSPQ--\n+------NK-RR---------------------------------------\n+--------------\n+>4577.GRMZM2G001079_P02\n+MGSSTDH-----AAGA---R-GKKQ-----G-S-QLWKKALLHSSLCFVM\n+GFFTGFAPSSVSDWTS----AA-----AAAGGRVGSSHVVRA---LP---\n+---------AG-G-AGAVNRSLLA-H---DA---GGGG---L-PRDPAS-\n+----------------------------PRPLLVVVTTTESTPAATGERA\n+AALTRAAHALRLVAPPLLWVVVEAAPDA--PATARLLRATGLMYRHLTYK\n+--DNFTSADAAAGRERHHQRNVALGHIEHHRLAGVVLFAGLGDVFDLRFF\n+DELRGIS-AFGAWPVATMRRGERKVVVRGPACSSAAVTGWFSQDLGGS--\n+GTA----AASAST-----ARPGELDVHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSMKFVQQVVLEDFSKVKGIPS-DCSEVMVWHVDTAAPSLQNKKRR\n+--------------------------------------------------\n+--------------\n+>4555.Si036401m\n+MGSSTDH----GGAGG---R-GKKQ-----G-S-QLWKKALLHSCLCFVM\n+GFFTGFAPSSVSDWTS----AA-----VSAG-GMGSSHVVRA---L----\n+--------------GGAVNRSLLA-H---GA---AVGG---AGL-LGDAG\n+LL-------GDA----AAS---------PRPLLVVVTTTESTPAASGERA\n+AALTRMAHTLRLAPPPLLWVVVEAATDV--PATARLLRTTGLMYRHLTYK\n+--DNFTAADAAAGKERHHQRNVALGHIEHHRLAGVVVFAGLGDTFDLRFF\n+DQLRQIS-AFGAWPVATMARDARKVVVRGPACSSSAVTGWFSLDFSNGTA\n+--------ASATT-----ARPPEVDAHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSMKFVQQVVLEDFSKVKGIPS-DCSEVMVWHVDSTAPSSSS----\n+--------------------------------------------------\n+--------------\n+>4558.Sb01g038640.1\n+MGSSTDH----GGAGG---R-GKKQ---A-GGS-QLWKKALLHSSLCFVM\n+GFFTGFAPSSVSDWTS----AA-----VAAG-RVGSSHVVRA---LPTAA\n+--------AAG-G-SGAVNRSLLA-H---GA---AGGL---LGLGDP-AS\n+----------------------------PRPLLVVVTTTESTPAASGERA\n+AALTRMAHTLRLVGPPLLWVVVEAAPEV--PATARLLRATGLMYRHLTYK\n+--DNFTAADAAAGKERHHQRNVALGHIEHHRLAGVVLFAGLGDVFDLGFF\n+DQLREIS-AFGAWPVATMWRDERKVVVRGPACSASAVTGWFSQDFSSNVN\n+GTA----PASAST-----ARPSEVDVHGFAFNSSVLWDPERWGRYPTSEP\n+DKSQDSMKFVQQVVLEDLSKVKGIPS-DCSEVMVWHVDTTAPSSSSSSQP\n+-S--MHNK-RR---------------------------------------\n+--------------\n+>15368.BRADI1G65750.1\n+MGSAALQDHAVGVGVG---R-AKKG---S-GGS-QLWKKALL'..b'P---\n+--------------------------------------------------\n+--------------\n+>29760.VIT_08s0040g02340.t01\n+MGSS-----------ER----SK---K---R-V-QLWKKAVVQFSLCFVM\n+GFFMGFAPAGKASFFS----SNAAA---LNQ-SQFSPQPVEM------LH\n+L---S---MT-PN-DGNGNRTLMA-E---TP---VEVPARSR-EVETA--\n+-E-------S--L-Q-E-GEDEPKL--VPGRLLIIVTPAGSE---DPSRG\n+VLLRRLAYTLRLVPPPLLWIVVEAQTDS--SEVSEILRKTGIMYRHLVSK\n+--ENFTEPAA----EMDHQRNLALSHIEHHKLSGIVHFAALSNVYDLRFF\n+DEIRDIE-YGIPYPSR----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------\n+>3694.POPTR_0006s13320.1\n+MGSL-----------ER----SK---K---K-V-QLWKKAIVHFGLCFVM\n+GFFTGFAPGGKASIFS----SHVVA---SNK-S----QPVEM----LHQQ\n+V---A---ST-PH-ASNVNRSLIA-E---S---PVPTPLSSK-ESEPA--\n+-K-------F--L-E-KEEEPKPKL--LPRRLAIIVTPISTE---DPYQG\n+VFLRRLANTIRLVPPPLLWIVVEGQSDS--DEVSEILRKTGIMYRHLVIK\n+--ENFTDPEA----ELDHQRNVALRHIEQHRLSGIVHFAGLSNVYDLGFF\n+DELRQIE-VFGTWPVALLSANKNKVTIEGPVCDSSQVIGWHLKKMNNETD\n+-------------------KRPPIHISSFGFNSSILWDPERWGR-PSSVQ\n+QTSQNSIKFVKQAALEDETELKGIPPEDCSKIMLWRLNLPVSKSPSYHLS\n+-TTGSTDA-SRRKI------------------------------------\n+--------------\n+>3694.POPTR_0016s08770.1\n+MGSV-----------ER----SK---R---R-V-QLWKKAIVHFGLCFVM\n+GFFTGFAPAGKASIFT----SHVAA---SNK-SQSLPQPVEM---TLHQQ\n+A---A---ST-PH-ASNVNRSLIA-E---T---AVPAPPSSK-ESEHA--\n+-T-------F--L-G-K-EETESKL--APRRLAIIVTPTSTK---DPYQG\n+VFLRRLANTIRLVPPPLLWIVVEGQSDS--DEVSEVLRKTGIMYRHLVFK\n+--ENFTDPEA----ELDHQRNVALRHIEKHRLSGIVHFAGLSNVYDLGFF\n+DEIRQIE-VFGTWPMALLSANEKKVIIEGPVCDSSQVIGWHLRKMNNETD\n+-------------------KRPPIHISSFGFNSSILWDPERWGR-PSSVQ\n+QTSQNSIKFVKQVALEDETKLKGIPPEDCSKIMLWRLNLPTSKSPSYQEN\n+-QEDKIV-------------------------------------------\n+--------------\n+>3847.GLYMA19G36280.1\n+MGSL-----------ER----SK---K---K-V-LLWKKAMLHFSLCFLM\n+GVFTGLAPTGKSSLFS----TKVAV---SNR-TEFAPQPSEM---S----\n+-----------NL-TTNVNRIWIA-P---M---PDTMPVKPR-ILENE--\n+-K-------KKTT-K-LHAKKQPQL--KPRRLIIIVTPTSTK---LPHQA\n+VFLRRLANTIKLVPQPLLWIVVEAKTNS--TELPEILRKTGIMYRHVVFK\n+--ENFTELEA----ELNHQRNLALKHIEHHRLNGIVHFAGLSNVYDLQFF\n+HQLRDIE-VFGTWPTALLAAHRKKVKIEGPVCDSSQVIGWHLRNMNNETD\n+T------------------ITPPIHISSFAFNSSILWDPERWGR-TSSVQ\n+DTSQNSIKFVKQVVLEDEAKLKGIPPEDCSKILLWRFNFRARTITNH---\n+--------------------------------------------------\n+--------------\n+>3847.GLYMA03G33570.1\n+MGSL-----------ER----SK---K---K-V-LLWKKAMLHFSLCFVM\n+GVFTGLAPTGKSSLFS----TTVSV---SNR-TEFAPQPSEM---L----\n+-----------HL-TTNVNRSWIA-P---T---PDSMPVKPR-ILENE--\n+-K-------KTTT-KKLHVKAQPQL--KPRRLLIIVTPTSTK---LPHQA\n+VFLRRLANTIKLVPQPLLWIVVEAKTNS--KELPEILRKTGIMYRHVVFK\n+--ENFTELEA----ELNHQRNLALKHIEHHRLNGIVHFAGLSNVYDLQFF\n+HQLRDIE-VFGTWPTALLAAHRKKVKIEGPVCDSSQVIGWHLKNMNNETD\n+T------------------ITPPIHISSFAFNSSILWDSERWGR-TSSVQ\n+DTSQNSIKFVKQVVLEDEAKLKGIPPEDCSKILLWRFNFRARTH------\n+--------------------------------------------------\n+--------------\n+>3847.GLYMA10G05730.1\n+MGSL-----------ER----SR---K---K-V-MLWKKAMVHFSLCFVM\n+GFFTGFAPTGKSIFHS-----HVDY---SNR-SEFAPQPIEM---S----\n+---------Q-KT-LTNVNRSWIA-P---T---ARSLVHKQ---------\n+------------NTK-LHVKIVPQL--KPRRLIIIVTPTSTK---HPFQT\n+VILTRLANTIKLVPQPLLWIVVEGQTDS--TELWKMLRKTGIMYRHLVSK\n+--ENFTDLEA----ELNHQRNLALKHIVHHRLSGIVHFAELSNVYDLEFF\n+QQLRHIE-VFGTWPTALLAANMKKVIIEGPVCDSSQVIGWHLRNMNNETD\n+T------------------ITPPIHISSFAFNSSILWDPERWGR-TSSLQ\n+DTSQNSIKFVKEVVLEDEAKLKGIPPEDCSRILLWRFNFHARTTSNHKFL\n+-TTTSGVI-RK---------------------------------------\n+--------------\n+>3847.GLYMA13G20080.2\n+MGSV-----------ER----SR---K---K-V-MSWKKAMVHFSLCFVM\n+GFFTGFAPTGKSIFHS-----HVDY---SNR-SEFAPQPIEV---S----\n+-----------QK-TTNVNRSWIA-P---T---PRSLVHKQ---------\n+--------------K-LHVKIGPQL--KPRRLIIIVTPTSTK---LPFQT\n+VILARLANTIKLVPQPLLWIVVEGQTDS--TELSKTLRKTGIMYRHLVSK\n+--ENFTDLEA----ELNHQRNLALKHIVHHRLSGIVHFAELSNVYDLEFF\n+QQLRYIDRVFGTWPTASLAANRKKVMIEGPVCDSSKVIGWHLRNMNNETD\n+I------------------ITPPIHISSFAFNSSILWDPERWGR-TSSLQ\n+DTSQNSIKFVKEVVLEDQEKLRGIPPEDCSRILLWRFNFHARTTSNHKFP\n+-TTASGVI-RK---------------------------------------\n+--------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.076.AA.strNOG.ENOG411BH75.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.076.AA.strNOG.ENOG411BH75.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,697 @@\n+>3218.PP1S7_412V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------MKEAS---------------\n+----E----ESVAPSV---P---AADP--K-A-QRGVLSVIWGLMGSLFS\n+RGNKNDFEKRLQHLTKEEVAVHSRLKRRTQRWRKLARVMIIYSIVGEALA\n+LGFAILSSRNADLPWQVRAIRALPVFALPAIVTLLYSTCAGFHRM-----\n+------MERKDHERLERLKTERQEKINELKEKTNYYITQQLI--------\n+--------------------------QQYDPDPAAKAAAASILASKLGAE\n+SGLKLALAAGLTSTDDLTQGKSSGAPNQSVGRLDREAMDHNSVGLRNRKS\n+QHRGQ-DFGPSS-QG-MPRM-EGFSRENN-MP-GG-PEVWEEQGMDVR-R\n+PPRNPSNG-GWIARLAAMLVGEDPTQCYALICKQCHAHNGLAKKEDYKYI\n+QYYCPHCRTL-NGTRPVEDGLSLTDEPAETSPKLELSKA-----------\n+-------------------------IASV-DG-ETLEISNPA-APALVSQ\n+LISGELDNSDSSEES-----------------------------------\n+---------------------------N\n+>3711.Bra010257.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------MA---QEQEGAVAE-TR-DQ\n+NDS----PVA--TATS---D---DSV-K-K-K-QNGFFSRIWNAMFR---\n+-DKGDDFEKRLEYISKEEANVLSRIKRRSITWRKLTRNLVLSSLFFEVIA\n+VGYAIMATRTKDLDWKMRSFRILPMFLLPALSALAYSSIVTFSKMF----\n+-------DRRDQRTLEKLRAERLDKINELKERTNFYITQQLIE-------\n+---------------------------RYDPDPAAKAAAATVLASKLGAD\n+SGLKVVLGD--ESLVDPAWGKSN----------DMEV--NQSRGLRNRRH\n+PNARPHSSAST-ST--HHSDDESR-HSGASERLLGTAEQNQQMDLTHYSP\n+EGYAAPDG-SWISRIAALLVGEDPTQSFAIICENCHMHNGLARKEDFAYI\n+TYYCPHCNALN-KPKYSEENPLLLPPVPAPLVTDSPSLI-----------\n+---------------------ETSELVNSSSS-SSERGNSPI-P-E----\n+--------------------------RKE-ETA------TTETGTP---S\n+----------------------------\n+>3702.AT4G31080.2\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------MA---QEQEGAVVE-KG-EP\n+NDSSAA-AVAATATAT---A---DSV-K-K-K-QNGFFSRLWNGIFR---\n+-VRGDDFEKRLQYISREEATVLSRMKRRSISWRKLTRNLIVSSVLFEIIA\n+VGYAILTTRTEDLDWRMRSFRILPMFILPAVSALAYSSIVSFSKMF----\n+-------DRRDQKTLEKLRAERLAKINELKERTNYYTTQQLIQAWHSHAT\n+KERSMFADLKRLTTACRAGANRIVLMQRYDPDPAAKAAAATVLASKLGAD\n+SGLKVYLGD--ESQLDPSSGKSN----------DMEV--NQSRGLRNRRQ\n+PNTRPHGSGST-ST--HHSDDESH-HSGTSERFPGTTEQNQQMLVEHYSP\n+QGYAAHDG-SWISRIAALLVGEDPTQSYALICGNCRMHNGLARKEDFAYI\n+TYYCPHCNALN-KPKHSEENVLL-PAISASPITDSLPLI-----------\n+---------------------ETSEVVNSSSS-SSERGSSPT-P-E----\n+--------------------------IKE-EAA------ITETGTP---S\n+----------------------------\n+>59689.fgenesh2_kg.7__1070__AT4G31080.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------MA---QEQEGAVVE-SD-VP\n+NDSVAA-AVAA--TAT---A---DSV-K-K-K-QKGFFSRLWNGIFR---\n+-VRGDDFEKRLQYISKEEATVLSRMKRRSITWRKLTRNLIVSSVLFEIIA\n+VGYAILTTRTEDLDWRMRSFRILPMFILPAVSALAYSSIVSFSKMF----\n+-------DRRDQKTLEKLRAERLAKINELKERTNYYTTQQLIQ-------\n+---------------------------RYDPDPAAKAAAATVLASKLGAD\n+SGLKVFLGD--ESQLDPSSGKSN----------DMEV--NQSRGLRNRRQ\n+PNTRPHGSGST-ST--HHSDDESH-HSGTSERFPGATEQNQQMLVEHYSP\n+QGYAAHDG-SWISRIAALLVGEDPTQSYALICGNCRMHNGLARKEDFAYI\n+TYYCPHCNALN-KPKHTEENALL-PAVSASPITDSLPLI-----------\n+---------------------ETSEVVNSSSS-SSERGNSPA-P-E----\n+--------------------------IKE-EAV------TAETGTA---S\n+----------------------------\n+>3711.Bra032104.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------MASVEKDHEGTVAD-TG-DQ\n+NDS----AAVP--SETVGGGEKKTTT-T-T-K-GKGMFSRIWNWIFR---\n+-VKGDDFEKRLKGISKEEATIRSRMKRRSVTRRKLIRNLIAFSVFFEVIA\n+VSYAIMTTRDEDLDWKLRSFRILPMFLLPALSFLTYSSLVSFTRMC----\n+-------DRRDQNTLEKLQGEMLGKIDELKERTNYFTTLDILR-------\n+---------------------------RFDPDPAARAAAATILASKLGAD\n+SGLKVYVGD--ESQLDPATGKSN----------DMEI--KHSHGLRNRKQ\n+PNAKRSVAGTTSST--HHSDNESN-HSGTSEGT--T-EQNQQMAFEHFNP\n+QGYAAHDG-SWISRIAALLVGEDPTQSYALICGNCHMHNGLCRKE'..b'----------------\n+----------------------------MA------------S-SPE---\n+--A-AAVGEEE--KGK---G---KRE-EGRR-G-GGVLGRMWRALFG---\n+-RR-EDYEKRLQYLSKEEAAVHARMRRRTQFSRTAVRNLIVLSVLAEVVA\n+IVYAIMTTRNEDITWEMRAIRVLPMFVLPAVSSVIYSTVVKFTRML----\n+-------ERKDQKTLEKLRAERKAKIDELKERTNYYLTQQLI--------\n+--------------------------QKYDLDPAAKAAAASVLASKLGEE\n+TGLKVHVGE--EPKLDSAVARSN----------DVEI--LPSEGLRNRKQ\n+SNARGSRTGGTT-AAQNPAQGAES-SL---TSSSGLEQ--PPMVVEHF--\n+QGSGASDG-GWIAKIAALLVGEDPSQSYALICGNCHMHNGLARKEDYPHI\n+TYYCPHCHALN-TSKQSLGQHSGSNSGWSTPVAPADGI------------\n+-------------------------SASSSVV-ESEVSNMT---------\n+--------------------------------TIQELKNEENTEKQEVQA\n+S---------------------------\n+>4577.GRMZM2G153332_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------MA------------A-SP----\n+--A-EAGAQAL--PEA---T---EAK-EKGK-R-GGVLRRVWRALFG---\n+-GR-EDFEKRLQYLSKEEAAVHARMRRRTQFSRRTVRNLIVLSVLAEVLA\n+VVYAIMMTRNEDLTWQMRAIRVLPMFVLPVVSSVIYSTVVNFTRML----\n+-------ERKDQKTLEKLRAERKAKIDELKERTNYYLTQQLI--------\n+--------------------------QKYDLDPAAKAAAASVLASKLGED\n+TGLKVHVGE--EPKLDAAVARSN----------DVEI--VPSDGLRNRKQ\n+PNARGSRTGSPT--ADTPARGTES-SL---TAGADLETAPAPLVVEHH--\n+QGLGASDGGGWIAKIAALLVAEDPSQSYALICGNCHMHNGLARKEDYPHV\n+TYYCPHCHALN-TSKQSMWQYSGSNSGRSSPVVLDDGL------------\n+-------------------------STSSSVQ-ETELSNLT---------\n+---------------------------------------------HTAGA\n+T---------------------------\n+>4555.Si016745m\n+MRVLTCLGRPSARGWPGVRAHAAAHPVPCQLLQRSLPEVYSQRHLRFQKP\n+FGLGCCSPAPENHPHLYVIRHRKPRDRLRGVRNLNGWCRHGTPGLHGLTR\n+APVPFQHFLPRTHLESELGTPSRPSYPKATGAGTRQPPPQTPPPPPPLFP\n+PSLPFGSRPEATSWPARVPTPTGSSAAGIHTANDQ--M-A--S-SPAAAA\n+AEE-VAPAPAP--PEA---A---EAK-GKGK-R-GGVLGRMWRALFG---\n+-GR-EDFEKRLQYLSKEEAAVHARMRRRTQFSRRAVRNLIVLSVLAEVLA\n+VVYAIMMTRDEDLTWQMRAIRVLPMFVLPAVSSLIYSTVVNFTRML----\n+-------ERKDQKTLEKLRAERKAKIDELKERTNYYLTQQLI--------\n+--------------------------QKYDLDPAAKAAAASVLASKLGEE\n+TGLKVHVGE--EPKLDAAVARSN----------DVEI--LRSDGLRNRKQ\n+PNASGSRTGSPS-GAHTPAHGTES-SP---TASAGLETAPAPMVVEHH--\n+QGTGASDG-GWIAKIAALLVGEDPSQSYALICGNCHMHNGLARKEDYPHV\n+TYYCPHCHALN-TSKQSMGQYSGSNSGQSTPAVPADGM------------\n+-------------------------STSSSVQ-EGELSNLT---------\n+--------------------------------TLQELPKEGNAEKQETEA\n+S---------------------------\n+>4577.GRMZM2G074436_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------MA------------S-TQ----\n+AEA-EAGAPAP--PEA---A---EAK-EKGK-Q-GGVLGRVWRALFG---\n+-GR-EDFEKRLQYLSKEEAAVHARMRRRTQFSRRAVRNLIVLSVLAEVLA\n+VVYAIMTTRNEDLTWQMRAIRVLPMFILPAVSSVIYSTVVNFTRMF----\n+-------EQKDQKTLEKLRAERKAKIDELKERTNYYLTQQLI--------\n+--------------------------QKYDLDPAAKAAAASVLASKLGEE\n+TGLKVHVGE--EPKLDAAVARSN----------DVEI--VPSDGLRNRKQ\n+PSARGSRTGSPT--SHTPAQGTET-NLPPAPASAGLETAPAPVVVEHH--\n+QGSGASDGGGWIAKIAALLVGEDPSQSYALICGSCHMHNGLARKEDYPHV\n+TYYCPHCHALN-TSKQSMGQYSGSNSGRSTPVVLADGL------------\n+-------------------------STSSSVQ-ETELSNLT---------\n+--------------------------------TLQELPEEGKTDKQQVEA\n+S---------------------------\n+>4558.Sb04g026710.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------MA------------S-SP----\n+AEA-EAEAGA---------P---EAA-EKGK-RGGGVLGRLWRALFG---\n+-GR-EDFEKRLQYLSKEEAAVHARMRRRTQFSRRAVRNLIVLSVLAEVLA\n+VVYAIMMTRDEDLTWQMRAIRVLPMFILPAVSSAIYSMIVNFTRML----\n+-------ERKDQKTLEKLRAERKAKIDELKERTNYYLTQQLI--------\n+--------------------------QKYDLDPAAKAAAASVLASKLGEE\n+TGLKVHVGE--EPKLDAAVARSN----------DVEI--VPSDGLRNRKH\n+PNARGSRTGSPT--AHTE-----P-S---LPANAGLETARAPMVVEHH--\n+QGSGASDGGGWIGKIAALLVGEDPSQSYALICGNCHMHNGLARKEDYPHV\n+TYYCPHCHALN-TSKQSMGQYSGSDSGQSTPVVLADGL------------\n+-------------------------STSSSVQ-ETELSNLT---------\n+--------------------------------TLQELPEEGNAEKREVEA\n+S---------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.077.AA.strNOG.ENOG411BH79.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.077.AA.strNOG.ENOG411BH79.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,1450 @@\n+>3711.Bra014193.1-P\n+----M-DK----P-----L-GTFFILLLIS--------------------\n+-------------PIVVATINEETSFPENAHLTN--------NLDQKC--\n+-------V-DIIKVDPSLKFENDRLKRAYIALQAWKK-AIYSDPFKTTKN\n+WVGPDVCSYNGVYCAEALD----DPS-LKVVAGVDLNYADIAGHLPAELA\n+LITDLAMFHINSNRFCGIIPKSLSKLALMYEFDVSNNRFVGPFPEVSLSW\n+PSLKFLDLRYNEFEGCLPSEIFDKNLDAIFLNNNRFESVIPDTIGKSAAS\n+VVTFANNKFSGCIPRSIGQMKN-LNEVIFTGNNLTGCFPNEIGSLNNVTV\n+FDASNNGFIGSLPLTLSSLSRVEQLDLSNNKLTGSVVDTFCKLPNLERFK\n+FSYNYFNGEAESCVH-GKNNGKQ----FDDRSNCLKNRPDQKSVNQCVPV\n+VSRP-VDCSKDKCSGGS------------QGG-SPPS---I-KT-P--EI\n+-I---PPKPK----EL--------------VIPK------PEESPKPEPQ\n+NPLRPETP--TTNVQQPIPEHEP-P---------K-----HE-S------\n+--PKP-----ENP--TNKP-----ELPKPEETPKPQPPK-SEE---SPKP\n+EPP--KT----------------SETPE-----------PVS--------\n+-PPKEDPYNASPVKNRRPPPPPPPKVK-----EI-----------QV---\n+-------------------PPP---------QPPMPSSPPPPV-------\n+--------------------------------------------------\n+---------------------YSSPPPP-------AP-------------\n+--INS-------PPP-------PVASPP-PPSP--P----PPVNS-----\n+------------------PPPPLIFSPPPPSPVYSPPPPIHSPPPPAHII\n+--IQP-P------------------IQAPTPV------QA----------\n+P---SSESDQSPVSSPVQSPTPIQS-----------PTP--S--------\n+----------------SVLDQ-----------------------------\n+--------------------------------------------------\n+-----------------------P----------------TID-AQ---S\n+PGQ-T--------------------------------------------P\n+TPLNEPASSPKEAED-RDAPEPSLSTPS--PSP-SPS--ENVAPPPENN-\n+--------NHSGFNLPPHIGFGYGSPPPPMFPGY---------------\n+>3702.AT1G49490.1\n+----M-ER----P-----F-GCFFILLLISYT-V----VATFDDE----P\n+-S---F----------------------------PENADLTKDLEQKC--\n+-------F-SINKVDPNLKFENDRLKRAYIALQAWKK-AIYSDPFKTTAN\n+WVGSDVCSYNGVYCAPALD----DDS-LTVVAGVDLNHADIAGHLPPELG\n+LMTDLALFHINSNRFCGIIPKSLSKLALMYEFDVSNNRFVGQFPEVSLSW\n+PSLKFLDLRYNEFEGSLPSEIFDKDLDAIFLNNNRFESVIPGTIGKSKAS\n+VVTFANNKFSGCIPKSIGNMKN-LNEIVFTGNNLTGCFPNEIGLLNNVTV\n+FDASKNGFVGSLPSTLSGLASVEQLDLSHNKLTGFVVDKFCKLPNLDSFK\n+FSYNFFNGEAESCVP-GRNNGKQ----FDDTNNCLQNRPSQKPAKQCLPV\n+VSRP-VDCSKDKCSGGS------------NGG-SSPS---P-NP-P--RT\n+-S--EP-KPS--KPEP--------------VMPK------PSDS------\n+--SKPETP--KTP-EQPSPKPQP-P---------K-----HE-S------\n+--PKP-----EEP--ENKH-----ELPKQKESPKPQPSK-PED---SPKP\n+EQP--KP----------------EESPKPEQPQIPEPTKPVSPPNEAQ--\n+GPTPDDPYDASPVKNRRSPPP--PKVE-----DT-----------RVPPP\n+QPPMPSPSPPSPIYSPPPPVHS---------PPPPVYSSPPPPH--V---\n+--------------------------------------------------\n+--------------YSPPPPVASPPPPS-------PP------------P\n+PVHSPPPPPVFSPPP-------PVFSPP-PPSPVYSPPPPSHS-------\n+------------------PPPPV--YSPPPPTFSPPPT---------HNT\n+--NQP-P------------------MGAPTPT------QAP-TPSSETTQ\n+VPTPSSESDQSQILSPVQAPTPVQS-----------STP--S--------\n+----------------SEPTQVPT-------------PSS---S------\n+----------------------ESYQAPN---------LSPVQAPTPVQA\n+PTTSSETS--Q-----------VP----------------TPS-SESNQS\n+PSQAPTPILEPVHAPTP---------------------NSKP-VQS---P\n+TPSSEPVSSPEQSEE-VEAPEPTPVNPSSVPSSSPST--DTSIPPPENND\n+DD------DDGDFVLPPHIGFQYASPPPPMFQGY---------------\n+>59689.fgenesh1_pg.C_scaffold_5000901\n+----M-EI----C-----I-E--LVKLTVDFV-A----AVAESIE----V\n+-A--FR-HRPPPVIQYSPVMYGRRILDESWPIIFDPSSNSMQLPKQQL--\n+-------I-SSIKSIPNLKFENDRLKRAYIALQAWKK-AIYSDPFKTTAN\n+WVGSDVCSYNGVYCAPALD----DDS-LTVVAGVDLNHADIAGHLPPELG\n+LITDLALFHINSNRFCGIIPKSLSKLALMYEFDVSNNRFVGQFPEVSLSW\n+PSLKFLDLRYNEFEGSLPSEIFDKDLDAIFLNNNRFESVIPGTIGKSKAS\n+VVTFANNKFIGCIPKSIGNMKN-LNEIVFTGNNLTGCFPNEIGLLNNVTV\n+FDASKNGFVGSLPTTLSGLASVEQLDLSHNKLTGFVVDKFCKLPNLESFK\n+FSYNFFNGEAESCIP-GRNNGKQ----FDDTNNCLQNRPSQKPAKQCLPV\n+VSRP-VDCSKDKCSGGS------------NGG-SSPS---P-NP-P--RT\n+-S--EP-KPS--KPEP--------------VVPK------PSESPKPEPQ\n+KPSKPQTP--KTP-EQPSPIPQP-P---------K-----HE-S------\n+--PKP-----EEP--ENKP-----ELPKQEESP-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--'..b'SYNFFTGEPPVCLS-L----PD----FSDRRNCLPARPLQRSAAQCNAF\n+LSRP-VDCSSFRCAPF-V-----------PSL-PPPP---PP-S-PP---\n+M-------PVP---------------------------SPPP--------\n+----------------------PP---------P------V-YS------\n+--PPPP-RP-S---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------------SSP-------\n+-------------------------------------PP-----------\n+--P-----------------------------------------------\n+--------------------------------------------------\n+--IHYKPPPS-------PS---PP--------------PPPAVYYHSPP-\n+--P-----------------------------------------------\n+---LSP-------------------------PPPPVI--YGSPPPPTPVY\n+E-----------GPLPPITGVSYASPPPPPFY-----------------\n+>3694.POPTR_0028s00200.1\n+--------------------------------------------------\n+------------------------MY--------IDKRQLLYYKDEFG--\n+-----DRG-ERVTVDPSLVFENPRLKNAYMALQAWKQ-AIFSDPLNLTAN\n+WVGSQVCNYEGVFCSRAPD----NKT-IRTVAGIDLNHGDIAGYLPEELG\n+FLVDLALFHINSNRFCGTIPHKFKKLRLLFELDLSNNRFAGKFPQVVLKL\n+PSLKFLDLRFNEFEGTVPKELFDKDLDAIFINHNRFVFDLPVNFGNSPVS\n+VIVLANNKFHGCVPSSLGNMSN-LNEIILMNNGFRSCLPAEIGLLKNLTV\n+FDVSFNQLIGPLPDTVGGMVSLEQLNVAHNMLSGKIPASICQLPNLENFT\n+FSYNFFTGEPPVCLS-L----PD----FSDRRNCLPGRPEQRSAAQCKAF\n+LSMP-VDCSSFRCAPF-V-----------PSL-PAPP---PP-S-PP---\n+V-------PVL---------------------------SPPP--------\n+PVVIPKSP--P------AP---PP---------P------V-YS------\n+--PPPP-PV-YSPPP----------------------LP-PVY---SPPP\n+PPP--PP---------------P-CI------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------EPPPPSP-------\n+-------------------------------------PP-----------\n+--P-------------IHYSPPQ---------------------------\n+--------------------------------------------PRP---\n+--VHYRSPPR-------PS---L----------------LPPVNYHSPP-\n+--P---P----S---LP---------------------PPIP-CEN---P\n+PPPPPP-------------------------PPPPII--YGSPPPPTP--\n+-------------------------------V-----------------\n+>3694.POPTR_0024s00730.1\n+--------------------------------------------------\n+------------------------MY--------INKRQLLYYKDEFG--\n+-----DRG-ERVTVDPSLVFENPRLKNAYMALQAWKQ-AIFSDPLNLTAN\n+WVGSQVCNYEGVFCSRAPD----NKT-IRTVAGIDLNHGDIAGYLPEELG\n+FLVDLALFHINSNRFCGTIPHKFKKLRLLFELDLSNNRFAGKFPQVVLKL\n+PSLKFLDLRFNEFEGTVPKELFDKDLDAIFINHNRFVFDLPVNFGNSPVS\n+VIVLANNKFHGCVPSSLGNMSN-LNEIILMNNGFRSCLPAEIGLLKNLTV\n+FDVSFNQLIGPLPDTVGGMVSLEQLNVAHNMLSGKIPASICQLPNLENFT\n+FSYNFFTGEPPVCLS-L----PD----FSDRRNCLPGRPEQRSAAQCKAF\n+LSMP-VDCSSFRCAPF-V-----------PSL-PAPP---PP-S-PP---\n+V-------PVL---------------------------SPPP--------\n+PVVIPKSP--P------AP---PP---------P------V-YS------\n+--PPPP-PV-YSPPP----------------------LP-PVY---SPPP\n+PPP--PP---------------P-CI------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------EPPPPSP-------\n+-------------------------------------PP-----------\n+--P-------------IHYSPPQ---------------------------\n+--------------------------------------------PRP---\n+--VHYRSPPR-------PS---L----------------LPPVNYHSPP-\n+--P---P----S---LP---------------------PPIP-CEN---P\n+PPPPPP-------------------------PPPPII--YGSPPPPTPVY\n+E-----------GPLPPVTGVSYASPPPPPFY-----------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.078.AA.strNOG.ENOG411BH99.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.078.AA.strNOG.ENOG411BH99.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,903 @@\n+>3218.PP1S251_85V6.1\n+--------------------------------------------------\n+--------------------------------MRLDSSATTVASPASESF\n+WRVGLLQTRERSPASLGRIVDRDKEEGRRREVGRRREEERERAQ-ERKRD\n+FKLHSRDV-RS-QSIPATTLASAPPAYSLCPPTFSVGYALTTKKIKSFMQ\n+PKLEELARSKGILLVAIEHSIPLIEQGPFDVLLHKN-----TGQEWRQSL\n+EDYKRKYPDVVVLDPPEAILQLRDRQSMLRDVAELDLSNAEGFVGVPKQL\n+VVT--GNATSISDSVSAAGLKLPLVAKPLVADGSPKSHAMSLVYDKSCLS\n+QLDPPLVLQEFVNHG-----------------------------GVVFKT\n+YVVGDYVRVVRRFSLPDVPEGE-TNRSGVVPFPRVSCAAESAEEAEEAGI\n+LDPQAA---------ELPPGPLLDSLSKGLRQKLGLHLFNMDIIRERGAG\n+NRYYVIDINYFPG------------FGKMPDYEKVFTDFLSDMA------\n+-VKRSKKISRID-----------------------------------S--\n+S--AIL--------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n+>3218.PP1S584_9V6.1\n+--------------------------------------------------\n+--------------------------------MRLDKNATSVASSASESL\n+WGVGLLQSRERSPLSLTRIVDREREEGRRREENRRREQEREREK-ERKRE\n+SKVYSRDG-RS-QITPVMALAPPSPTFTLPPPTFSVGYALTSKKIKSFVQ\n+PKLEELARSKGISLVAIDRSIPLTEQGPFDVLLHKS-----TGKEWRQSL\n+EDYKRLYPDVVVLDPPEAILQLRNRQSMLQDVAELDMSDAGGYVGVPKQL\n+VVT--GDATSIPAAVSEAGLKLPLVAKPLVADGSPKSHAMSLVYDESCLT\n+QLDPPLVLQEFVNHG-----------------------------GVLFKT\n+YVVGDYVRVVRRFSLPDVPEGEMKRN-GIMPFPRVSCAAESAEEALAAGI\n+LDPQAA---------ELPPRRLLESLSKELRRRLGLQLFNMDIIREGGAG\n+SRYYVIDINYFPG------------FGKMPEYEKVFTDFLVDLA------\n+-VNKSKKTSRAD-----------------------------------S--\n+S--V-C--------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n+>3711.Bra034582.1-P\n+--------------------------------------------------\n+--------------------------------MFGT--------------\n+----------------------------------LASGELET-A-RLRRD\n+L----GFS-C-----------GGIRMEGEQTQKLVVGYALTPKKKKSFLQ\n+PKLEVLARRKGICFVPIDLNRPLSEQGPFDVVLHKL-----LGKEWQDVI\n+EDYQQKHPEVTVLDPPGAIQRIHNRQSMLEGLADLNLSDCSGSIFVPKQM\n+VVL--KDSASSADRAVEAGLKFPLVAKPLWIDGTAKSHQLFLAYDRRSLA\n+ELDPPLVLQEFVNH-----------------------------GGVMFKV\n+FVVGDTIKVVRRFSLPNISNCEKGKVDGVFQFPRVSSAAASADNAD----\n+LDPSVA---------ELPPKPFLEALAKELRILLRLRLFNIDMIREHGSK\n+NVFYVIDINYFPG------------YAKMPDYEQVFVDFFHDM-------\n+AQAKQKKRHSTLLLPTMSLLLRTLPLRPSLFLSATANAAVLFLLPKLR--\n+NPLPRTRRTFSNSTAAATSIDSVVKPPPLPLPPSLLRWVSRTELCGELSV\n+EDVGKRVHLCGWVALHRVHGGLTFLNLRDHTGIVQVRTLPDEFPEAHGLI\n+NDMRLECQMLSQNRLSGFSRRPLKVLCVPLGAKRYSNSALKKGDVYNEAI\n+KSGAKGLPFLKILDNGEVEGIAALVSSLDPEGKANIVRQCGAKPGDLILF\n+GVGPVTSVNKTLDRLRLFVAHDMDLIDHSKHSILWVTDFPMFEWNEPEQR\n+LEALHHPFTAPRPEDIDDLPSARALAYDMVYNGVEIGGGSLRIYKRDGQE\n+KALEIIGISAEEAEAKFGYLLEALDMGAPPHGGIAYGLDRMVMMLGGASS\n+IRDVIAFPKTTTAQCALTRTPSEVDPKQLQDLSIRTK\n+>3711.Bra013122.1-P\n+--------------------------------------------------\n+--------------------------------MRVEE-E--DSM------\n+----------------------------------VPQG---N-E-AD-GE\n+M----VLD-T-----------A---SSQHQEEKLVIGYALTSKKKQSFLQ\n+PKLEVLARKKGISFVSIDQDKPLSEQGPFDVVLHKL-----LGNEWHDVI\n+QDYQKTHPEVTVLDPPGAIQRIYNRQSMLQGLADLNLAECDGMICVPKQM\n+VVL--QDTTSSGNEVAKAGLKFPLVAKPLLVDGTAKSHQLFLAYDCLSLA\n+ELEPPLVLQEFVNH-----------------------------GGVLFKV\n+FVVGDVIRVVRRFSLPNVSNVEKEEVAGVFQFPRVSSAAASVDKTD----\n+LDPRVA---------ELPPKPLLKGLVRELRSRLGLRLFNIDMIREHGSQ\n+DVFYVIDINYFPG-K---FFYLFFWYGKMPDYEQVFIDFFLGL-------\n+AQAKHEKKGL----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------CVKSGIEK----------------\n+----------------------------------'..b'VVGYALTSKKVKSFLQ\n+PKLEGLARSKGILFVAIDQSKSLSDQGPFDIVLHKL-----SGTKWRRIL\n+EEYRLTHPDVTVLDPPDAIQQVYNRQYMLEDVADLNLSDTYGKVGVPRQL\n+VIE--KDSSSIPDAVGKADLRLPIVAKPLA----AKSHELSLAYDKFSLQ\n+MLEPPLVLQEFINHG-----------------------------GILFKV\n+YIVGEAVKVVRRFSLPDISKRELAKNPGVFRFPRVSCAAASADEAD----\n+LDPSV---------GELPPRPLLEKLAKELRRRLGLRLFNLDIIRELGTK\n+DRYYVIDINYFPG------------YGKMPEYEHIFTDFLLSL-------\n+VKQKQ---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n+>4081.Solyc04g077120.2.1\n+--------------------------------------------------\n+--------------------------------MRD---E-IVGY------\n+--------------------------------K--EEENYKK----EEER\n+E----M----------------VGGGLVESKKFVVVGYALTSKKVKSFLQ\n+PKLEGLARSKGILFVAIDQSKPLSDQGPFDIVLHKL-----SGSKWRRIL\n+EEYRLTHPDVTVLDPPEAIQHIYNRQYMLEDVADLNLSDTYGEVGVPRQL\n+VIE--KDSSSIPDAVGKAELRLPIVAKPLA----AKSHELSLAYDKFSLQ\n+MLEPPLVLQEFINHG-----------------------------GILFKV\n+YIVGEAVKVVRRFSLPDISKRELSTNPGVFRFPRVSCAAASADEAD----\n+LDPCV---------GELPPRPLLEKLAKELRRRLGLHLFNLDIIRELGTK\n+DRYYVIDINYFPG------------YGKMPEYEHIFTDFLLSL-------\n+VKQKQ---------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n+>3694.POPTR_0005s19370.1\n+--------------------------------------------------\n+--------------------------------MGLQG-Q-IIPY------\n+--------------------------------K--NG------EKEEDDD\n+E----RAGK---------EI-SPFPPPPLHSKFAVVGYALTSKKIKSFLK\n+PKLEGLARNKGILFVAIDQNRPLSDQGPFDIVLHKL-----TGKEWRQIL\n+EDYRRTHPEVTVLDPPDAIQHLHNRQSMLQCVADMNLSNSYGKVGIPKQI\n+VIK--KDASSIPGAVAKAGLMLPIVAKPLVADGSAKSHELSLAYDQQSLQ\n+KLEPPLVLQEFVNHG-----------------------------GVMFKV\n+YIVGETIKVVRRFSLPDVCKRELSNIAGVFRFPRVSCAAASADNAD----\n+LDPGV---------AELPPRPLLEKLARELCRRLGLRLFNLDIIREHGTR\n+DRFYVIDINYFPGES---TFSFIFCYGKMPEYEHIFTDFLLSL-------\n+VQNQYKKKS-----------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------T--------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n+>29760.VIT_18s0001g08310.t01\n+--------------------------------------------------\n+--------------------------------MRLN----M--N------\n+--------------------------------E--EG--------REEEE\n+E----MIQGR--------FSIGEGGGFQKPMKLVVVGYALTSKKTKSFLQ\n+PKLERLARNKGISFVAIDQNRSLSEQGPFDIVLHKL-----SGKEWRQIL\n+EDYRQTHPEVTVLDPPDAIQHVHNRQSMLQDVADLNLSNSYGKVGVPKQL\n+VVK--RDASSIPDAVTKAGLKLPLVAKPLVVDGSAKSHELSLAYDQYSLQ\n+KLEPPLVLQEFVNHG-----------------------------GVLFKV\n+YIVGEAIKVVRRFSLPDVTKRELSKNAGVFRFPRVSCAAASADDAD----\n+LDPCV---------AELPPRPLLERLARELRRRLGLRLFNLDIIREHGTR\n+DRFYVIDINYFPG------------YGKMPEYEHIFTDFLLSL-------\n+AESNYKRLS-----------------------------------------\n+G--SN---------------------------------------------\n+--------------------------------------------------\n+---------------------------G----------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.079.AA.strNOG.ENOG411BJDC.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.079.AA.strNOG.ENOG411BJDC.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,310 @@\n+>4513.MLOC_51654.2\n+ME-------MT--ARFL-AAAA--A----C-VWLA---AA--ASAFDVPT\n+VAFEEGFSPLFGDGNLVRARDDRAARLLLDRRSGSGFISSDYYLHGFFSA\n+SIKLPRDYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNV\n+YGNGSTSRGREERYLLPFDPTLAAHRYSILWAPTHIIFYVDDTAIREVVR\n+HPGMGGDFPAKPMAAYATIWDGSAWATEGGKYKVNYKYAPFASDFSDLSL\n+RGCRV-ADPASPAL-----RLAGG-DGC---D-LLGLMTADYAVMTPQKR\n+AAMRAFRARRMTYTVCYDAARYAAGPFPECDNSDEERGTFWAWGES----\n+KT-------VVM-K--T---------------------------------\n+-----------\n+>15368.BRADI3G52307.1\n+MA-------VK--ARFF-AAAMLAA----A-CLSA---AV--AAAFDVPS\n+VAFGEGFSPLFGDGNLARTPDDRTARLSLDRRSGSGFISSDYYLHGFFSA\n+SIKLPKDYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNV\n+YGNGSTSRGREERYLLPFDPTVEAHRYSILWAPTHIIFYVDDTPIREVIR\n+HAGMGGDFPAKPMAVYATIWDGSAWATEGGKYKVNYKYAPFASDFSDLAL\n+HGCRV-A-ATHDAG-------GAS-SGC---E-LLGLMTADYAVMTPRKR\n+AAMRAFRARQMTYTVCYDAARYAAGPFPECDNSDQEKEAFWAWGES----\n+KTVVMKTSRGRG-R--RGR--------GS-----K-----AGA-AKARA-\n+-----GVVASS\n+>39946.BGIOSGA008858-PA\n+MA-------LE--ARFF-LAAVFAV-AATC-LCLS---AV--ASAFAVPS\n+VAFDEGYSPLFGDDNLVRSSDDKSVRLLLDRRSGSGFISSDYYLHGFFSA\n+SIKLPKAYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNV\n+YGNGSTARGREERYLLPFDPTLEAHRYSVLWAPTHIIFYIDDTPIREVIR\n+HPGMGGDFPSKPMAVYATIWDGSTWATDGGKYKVNYKYAPFASEFSDLAL\n+LGCRA-D-PVLRAP-----RDGGG-AGCAEPD-LLGLLTADYAIMTPRKR\n+AAMRAFRARHMTYTVCYDAVRYAAGPFPECDVSDVEKESFSAWGES----\n+KNVVMKARGRGR-R--RGR--------KA-----G-----VAGAGAMSRL\n+-----DVSS-S\n+>39947.LOC_Os02g46910.1\n+MA-------LE--ARFF-LAAVFAV-AATC-LCLS---AV--ASAFAVPS\n+VAFDEGYSPLFGDDNLVRSSDDKSVRLLLDRRSGSGFISSDYYLHGFFSA\n+SIKLPKAYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNA\n+YGNGSTARGREERYLLPFDPTLEAHRYSVLWAPTHIIFYIDDTPIREVIR\n+HPGMGGDFPSKPMAVYATIWDGSTWATDGGKYKVNYKYAPFASEFSDLAL\n+LGCRA-D-PVLRAP-----RDGGG-AGCAEPD-LLGLLTADYAVMTPRKR\n+AAMRAFRARHMTYTVCYDAVRYAAGPFPECDVSDVEKESFSAWGES----\n+KNVVMKARGRGR-R--RGR--------KA-----G-----A---GAMSRL\n+-----DVSS-S\n+>4555.Si017659m\n+MA-------VK-------AA-LLLAAATWV-CLSAAAASA--FEFEDVPT\n+VAFDERFSPLFGDGNLVRSSDDRSVRLLLDRRSGSGFISSDYYLHGFFSA\n+SIKLPKDYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNV\n+YGNGSTSHGREERYLLPFDPTLEAHRYSVLWAPTHIIFYIDDTPIREVIR\n+HPDMGGDFPAKPMAVYATIWDGSAWATEGGKYKVNYKYAPFASEFSDLAV\n+VGPRA-D-PVLRFP-----RRAGAGADQ---D-LLGLMTADYAVMTPQKR\n+AAMRAFRARQMTYTVCYDAVRYASGPFPECDNSDEERENFSAWGES----\n+KTVVMRPRARGR-R--RGR--------KA-----G-----AGA-GAKGRT\n+-----GVAS-S\n+>4558.Sb04g031050.1\n+MA-------AK--ARVS-LT-VLLAAATLA-CLCA---VAASASAFDVPS\n+VAFEERFSPLFGDGNVVRSSDDRSVRLLLDRRSGSGFISSDYYLHGFFSA\n+SIKLPKDYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNV\n+YGNGSTSHGREERYLLPFDPTLEAHSYSILWAPTHIIFYIDDTPIREVIR\n+HPDMGGDFPAKPMAVYATIWDGSAWATDGGKYKVNYKYAPFASDFSELAV\n+VGFRA-D-PVLRVA-----HRHGA-RQA---D-LLGLMTADYAVMTPQKR\n+AAMRAFRARQMTYTVCYDAVRYADGPFPECDNSDEERESFSAWGES----\n+KTVVMRPRARGR-R--RGR--------KA-----G-----AGA-RVPPA-\n+-----DVSS-S\n+>4577.GRMZM2G060837_P05\n+MA-------AK--ARVS-LT-AVLAAAAWA-CLSV---VA--ASAFDVPT\n+VAFEEGFSPLFGDGNLVRSSDDRSVRLLLDRRSGSGFISSDYYLHGFFSA\n+SIKLPKDYTAGVVVAFYLSNGDVYEKTHDELDFEFLGSRWGGQWRVQTNV\n+YGNGSTSRGREERYLLPFDPTVEAHSYSILWAPTHIIFYVDDTPIREVIR\n+HPDMGGDFPAKPMAVYATIWDGSAWATDGGKYKVNYKYAPFASDFSELAV\n+VGSRA-D-PVLRVP-----RRDGA-AHQ---D-LLALMTADYAVVTPRKR\n+AAMRAFRARQMTYTVCYDAVRYADGPFPECDNSDEERESFSAWGES----\n+KTVVMRPRARGR-R--RGR--------KA-----G-----RGR-AGVSS-\n+----------S\n+>4081.Solyc01g081060.2.1\n+-------------MKI-CLS--VL--------FFFHVWFC--RAFNDVST\n+IPFNKGFSHLFGDGNILHANDDNSLQLHLNQNTGSGFKSSDLYNHGFFSA\n+KIKLPSDYTAGIVVAFYTTNQDVFKKTHDELDFEFLGNIKGKAWRFQTNM\n+YGNGSTHRGREERYTLWFDPSKEFHRYSILWTNKNIIFYIDDVPIREIVR\n+NDAMGGDYPSKPMGLYATIWDASDWATSGGKYKTNYKYAPFIAEFTDLVL\n+NGCAM-D-PLEQVV--------NPS-LCDE-K-DVELQKSDFSRITSRQR\n+MSMKRFRAKYMYYSYCYDSLRYS-VPPPECEIDPVEQQHFKETGRL----\n+KFINKHHGHRHP-KKTKSE--------VL------------DAR-KYGNE\n+--------DEE\n+>4113.PGSC0003DMT400004553\n+--MDF----IR--MKI-SLS--VL--------LFFHVWLC--RAFNDVST\n+IPFNKGFSHLFGDGNILHANDDNSLQLHLNQNTGSGFKSSDLYNHGFFSA\n+KIKLPSDYTAGIVVAFYTTNQDVFKKTHDELDFEFLGNIRGKAWRFQTNM\n+YGNGSTHRGREERYTLWFDPSKEFHRYSILWTNKNIIFYIDDVPIREIVR\n+NDAMGGDYPSKPMGLYATIWDASDWATSGGKYKTNYKYAPFIAEFTDLVL\n+NGCAM-D-PLEQVV--------NPS-LCDE-K-DVELQKADFSRITSRQR\n+MAMKRFRAKYMYYSYCYDSLRYS-VP'..b'SPDDRSVRLLLDKYTGSGFISSNMYQHGFFSS\n+LIKLPGAYTAGLVVAFYTSNGDVFVKNHDELDIEFLGNVEGKPWRFQTNM\n+YGNGSTNRGREERYRLWFDPSKEFHRYSILWNPTKIIFWVDDVPIREIIR\n+KEEMKGDYPQKPMSLYATIWDASSWATSGGKFGVDYAFSPFVSEFKDVAL\n+DGCNVSD-SFPNN--NNNTVGYNYV-NCSA-S-DQDLMASDYSTISPKQA\n+AAMRRFRERYMYYSYCYDTVRYA-VPPPECVIVTAEKDRFKDTGRL----\n+KFGGSHR----ARKRRKRN--------RS-----T-----PVVS---AD-\n+----------Q\n+>3711.Bra035513.1-P\n+--MSK----LS--YNLIFFI--VF--------LCLGLR-S--SAFTNLNT\n+LSFEESLSPLFGDGNLVRSPDDLSVRLLLDKYTGSGFISSNMYQHGFYSS\n+MIKLPADYTAGVVVAFYTSNGDVFEKTHDELDIEFLGNIKGKPWRFQTNL\n+YGNGSTHRGREERYRLWFDPSKEFHRYSILWTPHKIIFWVDDVPIREVIR\n+SEAMGADYPAKPMSLYATIWDASDWATSGGKYKANYKYAPFVAEFKSFSL\n+DGCSV-D-PIQEVP----------T-DCSD-S-VDFLESQDYFSINSRQR\n+AAMRRFRQRFMYYSYCYDTVRYP-EAPPECVIVPAEKDRFKDTGRL----\n+KFGGTEARGRRR-NRRQQR--------P-------------EIE-SDPDE\n+-----RRRLLK\n+>3702.AT1G32170.1\n+--MSK----SS--YNHIF---ILI--------LCLCLRSS--SAFTNLNT\n+LSFEESLSPLFGDANLVRSPDDLSVRLLLDRYTGSGFISSNMYQHGFYSS\n+MIKLPADYTAGVVVAFYTSNGDVFEKTHDELDIEFLGNIKGKPWRFQTNL\n+YGNGSTHRGREERYRLWFDPSKEFHRYSILWTPHKIIFWVDDVPIREVIR\n+NDAMGADYPAKPMALYATIWDASDWATSGGKYKANYKFAPFVAEFKSFSL\n+DGCSV-D-PIQEVP----------M-DCSD-S-VDFLESQDYSSINSHQR\n+AAMRRFRQRFMYYSYCYDTLRYP-EPLPECVIVPAEKDRFKETGRL----\n+KFGGTEARERRR-NRRQQR--------RP-----E-----IEIE-SDPDD\n+-----RKLL--\n+>59689.fgenesh2_kg.1__3352__AT1G32170.1\n+--MSK----SS--YNNIFFIIILI--------LGLGLRSS--LAFTNLNS\n+LSFEESLSPLFGDANLVRSPDDLSVRLLLDRYTGSGFISSNMYQHGFYSS\n+MIKLPADYTAGVVVAFYTSNGDVFEKTHDELDIEFLGNIKGKPWRFQTNL\n+YGNGSTHRGREERYRLWFDPSKEFHRYSILWTPHKIIFWVDDVPIREVIR\n+NDAMGADYPAKPMALYATIWDASDWATSGGKYKANYKFAPFVAEFKSFSL\n+DGCSV-D-PIQEVP----------V-DCSD-S-VDFLESQDYSSINAHQR\n+AAMRRFRQRFMYYSYCYDTLRYP-EPLPECVIVPAEKDRFKETGRL----\n+KFGGTEARERRR-NRRQQR--------RP-----E-----IEIE-SDPDD\n+-----RKLL--\n+>29760.VIT_02s0012g02220.t01\n+--MGQ----LP--VIRN-FSLFFF--------FFVSFFCA--ASSFNLSV\n+ISFDQGYTHLFGEGNLVRSSDGRSVRLLLDRYTGSGFISANLYNHGFFSA\n+NIKLPSEYTAGVVVAFYTSNGDVFEKTHDELDFEFLGNVKGKPWRFQTNV\n+YGNGSTSRGREERYRLWFDPSKEFHRYSILWTAKNIIFYVDEVPIREVIR\n+NEAMGGDYPSKPMALYATIWDASNWATSGGKYKVDYNYAPFVSEFSDFVL\n+DGCPA-D-PLQLA---------SAG-GCSD-K-DAELESNDYSAITPLRR\n+ISMRKFRQKYMYYSYCYDTLRYA-TPLPECVIIPSEKRRFKDTGRL----\n+KFGGSHKKSS----KRRSR--------VP-----V-----ATTT---SDR\n+-----Q--AAA\n+>3847.GLYMA09G34140.1\n+--------------------------------------------------\n+-----------------------------------------MYQYGFFSA\n+RIKLPSNYSAGICVAFYTSNGDVFEKSHDELDFEFLGNVAGKPWRFQTNL\n+YGNGSTNRGREERYRLWFDPTKEFHRYSILWTAKNVIFYIDEVPIREVLQ\n+SEEMGGDYPSKPMSLYATIWDASNWATSGGKYKVNYKYAPFVTEFKDLVL\n+KGCSA-D-PIQEVT--------GTK-SCSD-Q-HADLEAQDYAGVTPMRR\n+LTMRRFRQRYMYYSYCYDTLRYP-VPQPECVIVPSEKQRFKETGRL----\n+KFGGSHHRQS----RRRGR--------TT-----T-----PVDH---TDQ\n+--------GDM\n+>3847.GLYMA01G01770.1\n+MDHRLRCFVTI--PKIP-FLLLLS--------LILVFSYV--NAAFDLAT\n+IPFNDGYSPLFGDSNVVRSEDGNGVQLRLDRYTGSGFISSSMYQYGFFSA\n+RIKLPSNYTAGICVAFYTSNGDVFEKSHDELDFEFLGNVAGKPWRFQTNL\n+YGNGSTKRGREERYRLWFDPTKEFHRYSILWTAKNVIFYIDEVPIREVLR\n+SEEMGGDYPSKPMSLYATIWDASNWATSGGKYKVNYKYAPFVTEFKDLVL\n+KGCSA-D-PIQEVS--------GTE-SCSD-Q-HADLEAQDYAAVTPMRR\n+LAMQRFRQRYMYYSYCYDTLRYP-VPQPECVIVPSEKQRFKETGRL----\n+KFGGSHRRQS----RRRGR--------TT-----T-----PVDD---TDQ\n+--------GDM\n+>3694.POPTR_0001s01870.1\n+--MDCLCCWSL--SKPF-YLLLFL--------FSFPCIIA--SAAFNLST\n+ISFDEGYSPLFGDGNLVRSPDGRTARLLLDRFTGAGFISSKMYKYGFFSA\n+NIKLPGDYTAGLCVAFYTSNGDVFEKTHDELDFEFLGNTEGKPWRFQTNL\n+YGNGSTSRGREERYRLWFDPSKQFHRYSILWTAKNTIFYIDDVPIREVIR\n+SEEMGGEYPSKPMSLYATIWDASNWATSGGKYKVNYKYAPFVSEFKDFVL\n+EGCPS-D-PIEEFP--------SV--DCYE-S-YSRLESADYATITRRQR\n+SAMRKFRQRYMYYSYCYDSLRYP-VPPPECVVIPTEKDRFRDTGRL----\n+RFGGSHQGRKRR-SRRRGR--------VQ---------------------\n+-----------\n+>3694.POPTR_0003s09590.1\n+--MDCLCCWSV--SKPL-YLLLFF--------YFF-SCTA--KAAFNLST\n+ISFDEGYSPLFGDGNLVRSPDGRSARLLLDRFTGAGFISSRMYKYGFFSA\n+NIKLPGYYTAGLCVAFYTSNGDVFKKTHDELDIEFLGNTKGEPWRFQTNL\n+YGNGSTSHGREERYRLWFDPSKEFHRYSILWTAKNIIFYIDDVPIREVIR\n+NEEMGSEFPSKPMSLYATIWDASNWATSGGKYKVNYKYAPFVSEFKDLAL\n+EGCPS-D-PIEEFP--------SF--DCYE-SDIARLENADYATITRRQR\n+SAMRRFRQRYMYYSYCYDALRYP-VPLPECVIIPSEKERFRDTGRL----\n+KFGGSHQGGKRR-SRRRGR--------GR-----V-----QASN---LEY\n+-----D--PDM\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.080.AA.strNOG.ENOG411BJIF.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.080.AA.strNOG.ENOG411BJIF.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,496 @@\n+>3218.PP1S114_3V6.1\n+-----------M-AKFGAMSNLCASCFRLQLLELLIMVVKALYVGIITCK\n+-QLF----RFEVRFVCLEFYK-NCPRLSEMVDHYQCV-----LRATRGVL\n+AAPIFPGSGFLFATIIGELHEIHSAVCDFVLIARLLNATIVLPKIQSIPA\n+VKGGNSKVKSFGYLYDEQHFITAVKDDVRVVKLLPNSFRTRASLQKLPVK\n+TPTRFSSVQFYLDEVLPALSAHGACGLVFAKGGGLQEILPTELVEYQRLR\n+CRVAFHALRFREEIRGLGAQLVRRLEAHGRPYVVVHFGLERDVLAYHGCA\n+ELFQDLQTESIQYQRKKMLISAEIDGELRIDSHKQRHRGLCPLMPSEVGL\n+LLEAFGFRNDTQLYMAGTEITGGQRVVLPLRSMYPSLDDRFTLTTDQERF\n+ALYAVDQQRTPDTSEPGSVYSNAWKKLFVWGKNRPSGYSYP---------\n+-SQKGWWRSVGECEYGTEKYFASTPVEGETNDIQLLHAALDYIVSLDANT\n+YFPAFDKDRQGLPNMASLIMGHRLYQSASLKTFRPNRSVLSALLDQYPHD\n+HSQ-EWNSWTRAMREVLVDALRPEAIVHLAHTAKSELFLAHPFPECFCRI\n+GQL-IRAND-FRDLSE----DGELFWGRVRMCPA----------------\n+--------------------------------------------------\n+-------RTPSEH\n+>4081.Solyc06g059980.2.1\n+--------------MKSKIKWAALGGLVLSFASLIVHLFLAKSSA-DLVQ\n+YTAIT----VFTEDLTPTLAIRKSPAFRKLWRNVKSLEPLHPYPNPRSTY\n+PVAVEQNNGFIYAKISGSFEKIRNSIVDLVAISRLLNATLVIPEIQESAR\n+SKGISSNFKSFSYLYNEDQFIAALANDVTIVKSLPPILMEARRRKEYQIF\n+KPKSSASPRFYTSEVLPRLKKAKVIGLILTDGGCLQSALPSSMVEYQRLR\n+CRVSFHALQFRPEIEALGKLMVERLRASGQSYLAYHPGLKRDALAYHGCA\n+EIFQDVHTELIQYRRAQMIKQGIISEELNVDSHARKRNGSCPLMPEEVGL\n+LLRAMGYPPRTRIFLSGSETFGGQRVMIPLRAMYTNLVDRTSLCSKTELA\n+NLVGPETPLIPDPDQLLPVKS-PNQLKSEWDKSGPRPRPLPPPPDRPIYR\n+HEKEGWYGWVAEKDKEP----EPSLNDQREQAHRLLWDALDYIVSVDAEV\n+FFPGFDNDGSG-PDFASLVMGHRLYEMASARTFRPNRKYLAELFNTTVDH\n+LYY-PPRNWTFAVREHLNKSLAEEGLLKESNLSKTKFFLSHPIPECSCST\n+V-KATDIVHSG--KNN----NLHLLFEGQDECPKWMQQLRTQ--------\n+-EANADE-V-------DSQEDETDLEG----QSE---SEGYNGADA--IP\n+SLEQDEEMDPDD-\n+>3847.GLYMA06G14070.2\n+-----------M-PFLTKIKWVVLSVVTLSLASIIIHLSLTKLWAVNIVQ\n+YKALP----SLPEEFGSVLG-RQVIKNKKLWGSIESLETLQPNANARSNY\n+SVPKEQSNGFIYAKVFGGFAKIRSSIPDLVAISRILNATLVIPEFQESTR\n+SKGISSKFKSFSYLYNEEQFITFLKNDVIIAKSLPESLMERRRRNEIPTF\n+KPTSSASLNFYIEEILPKLKKSKVIGLIIADGGALQSILPLSMAEIQRLR\n+CRVAFHALQFRPEIQTLGRRMVHKLRALGQPFLAFHPGLLRETLAYNGCA\n+ELFQDVHTELIQHQRSQMIKEGILKDELNVDSHLRREKGLCPIMPEEVGI\n+LLRVMGYPAKTIIYLAGSELFGGQRALIPLRSMFINTLDRTSLCSEKELS\n+DLVGPETPLPVNSFRPPPTKS-EKELKEEWKKAGPRPRPLPPPPGRPIYQ\n+HEKEGWYAWITETPTEP----DPSPMDLRMKAHRLLWDALDYIVSLEADA\n+FFPGFNNDGSGWPDFSSLVMGHRLYETASFRTYRPDRKVVAELFNTTREN\n+LYH-PKHNWTILVQEHLNKSLTEEGLIRQSLLSKPAMFLSHPFPECSCRI\n+A-ST-KATNHV--KGE----NGQVLYGGEDICPKWMQHANDAGKLEKEGV\n+---KSQD-E-------GLADYESNDFV----DES---ESDKNGSKTSQTP\n+LWDQDEEMDPND-\n+>3847.GLYMA04G40730.1\n+-----------M-PFLTKIKWVVLSVVTLSLASIIIHLSLTKLWTVNIVQ\n+YKALP----SLPEEFGSVLG-RQVIKNKKLWGSIESLETLQPNANTRSNY\n+SVPKQQSNGFLYAKVFGGFSKIRSSIPDLVAISRLLNATLVIPEIQESTR\n+SKGISSKFKSFSYLYNEEQFIAFLKNDVIIAKSLPESLMERRRRNEFPTF\n+KPTSSASLNFYIKEILPKLKKSKVIGLIIANGGALQSILPPSMAEIQRLR\n+CRVAFHALQFRPEIQMLGRRMVHKLRALGQPFLAFHPGLLRETLAYNGCA\n+ELFQDVHTELIQHRRSRMIKEGVLKDELNVDSHLRREKGLCPIMPEEVGI\n+LLRVMGYPAKTIIYLAGSELFGGQRALIPLRSMFINTMDRTSLCSEKEFS\n+DLVGPETPLPVNSFRPPPAKS-ENELKEEWKKAGPRPRPLPPPPGRPIYQ\n+HEKEGWYAWITETPTEP----DPSPMDLRMKAHRLLWDALDYIVSLEADA\n+FFPGFNNDGSGWPDFSSLVMGHRLYETASFRTYRPDRKVVAELFNMTREN\n+LYH-PKHNWTVLVQEHLNRSLAEEGLIRQSLLSKPAMFLSHPLPECSCRI\n+A-ST-KATNRF--RGE----NGQVLYGGEDICPKWMQHANDEGSLEKEGS\n+---KSED-E-------GLADYESNDFV----DES---ESEKNGSKTNQTP\n+LWDQDEEMDPND-\n+>3711.Bra036430.1-P\n+-----------M-VFRSRIKWIALLVLILSVGSLLVHLSITKSSSVQLAS\n+-YARG----TLWQDFDSLLG-SQDFRNKHLWRPVRSLETLQPYANPRTSY\n+PAPSSANNGYIYAKIFGGFDKIRSSICDLVTISRLLNATLIIPELQESLR\n+SKGISNKFKSFSYLYDEEQFISFLKNDVIVAKTLPESLKAARKRNEFPLF\n+KPKNSASTKFYLEDVLPKLKKAGVIGLVVSDGGCLQSTVPASMPELQRLR\n+CRVAFHALQLRSEIQVLGKKMVDRLRRSGQPFLSYHPGLVRDKLAYHGCA\n+ELFQDLHSELIQYRRAQMIKQKFISEELIVDSHLRRDNGLCPLMPEEVGI\n+LLKALGYSQKAIIYLAGSEMFGGHRVLIPLRAMFPNLVDRTSLCSTEELS\n+ELVGPETPLPENTYEMPPRKS-DKQLKEEWNKAGPRPRPLPPPPDRPIYQ\n+HEKEGWSGWLTENDTEP----IPSPMDLRNQAHRLLWDALDFVVSVEADV\n+FLPGFNNDGSGLPDFSSLVMGQRLYERPSSRTYRLDRKVIQELFNITRED\n+MYH-PNRNWTVRVREHLNSSLGESGLIRQSMLSKPRLFLSHPLPECSCRT\n+S-PL-EESRQI--RSD----DGRFLYGGEDECPKWIKSAG--------VE\n+-KSKNDD-G-------DQPDYEHDLLP----EQS---ETEEEFAKSKVAS\n+AFDQDEEWDPND-\n+>59689.fgenesh2_kg.3__335__AT3G03810.1\n+-----------M-VFKSRIKWIALFVLILSMGSLVVHLSMTKSSGVQLAY\n+-SARD----NLWQDFDSLLG-AQDFRNKHLWRPVKSLETLQPYANPRNSY\n+PAPSSTN'..b'KLLKKSI-PEGLVESSKRSKAFSFLSHPVPECSCIK\n+RDH-RVSN----------VSLIEADLGVTHRCPQGMDGAV--RSKDNKNA\n+EKEEDLDEE-DLSSSGFFFGHKE-SGGSSNSNNE---TVNSEANNKEEGQ\n+LEDQEELEGGE-R\n+>3847.GLYMA08G28020.1\n+-----MKGEVK---MKSKMKWVGLLGLVLSAFSIFIHFLLARFTQMGVAE\n+YESSVTIFSWRPVFEKPIPP-TNTPSYRKLWGPVKRLESLYPDSNPRGHY\n+ADPVSETNGFIFVRIQGGFHEIRNSICDVVVVARLLNATLAMPEIQSTTS\n+SKGISSQFKSFAYLYNEEQFVLSLAKDVTVVRTLPKDLKGARRKKEIPVF\n+KVPYSASPFYYFHHVLPVLKKHSVVELVVSEGGCLKATLPPNFEEYQRLR\n+CRVSFHALQFRQEVQELSAKILQRLRAPGRPFIAFDPGMTRESLTYHGCA\n+ELFQDVHTELIQHKRSWMIKRGIVKGKLSVNSAEERLKGSCPLMPQEIGI\n+LLRAYGYSKDAIIYVSGGEVFGGQRTLIPLHAMFENVIDRTSLSTPWEMI\n+RLYGKEVNLVDT-PGPPPFVE-EVTKHAAWKSAGPRPRPLPPPPARPK-S\n+YNIEGWWGWVAESDNEP----DSTVIELRTNAHKLLWEAIDYVICVEADV\n+FIPGFDRDGKGHPNFASLVMGHRLYLSAASKTFRPDRKEVAKLLDEIRDH\n+GHH-ANHTWLESVRRHLKKTL-LDGIMEASNKSKLLSFLSHPVPECSCSR\n+-DS-FEVSKNS--SSPL-TSQLVTSLGVAHRCPAWMDTGPISQSKDK---\n+ENEEDVYED-DSVSE-LFFK--Q-N-A----ENH---EGDSEVNIKEENQ\n+FEDQEDD-SGE-R\n+>3847.GLYMA18G51090.1\n+-----MKGEVK---MKSKMKWVGLFGLVLSAFSIFIHFLLARFTQMGVAD\n+YESSVTIFSWRPIFEKPIPP-TNTPSYRKLWGPVKRLESLYPDSNPRGYY\n+ADPVSETNGFIFVRIQGGFHEIRNSICDVVVVARLLNATLAMPEIQSTTS\n+SKGISSQFKSFAYLYNEEQFVLSLAKDVTVVRTLPKDLKGARRKKEIPVF\n+KVPYSASPFYYFHHVLPVLKKHSVVELVVSEGGCLKATLPPNFEEYQRLR\n+CRVSFHALQFRQEVQELSAKILQRLRAPGRPFIAFDPGMTRESLAYHGCA\n+ELFQDVHTELIQHKRSWMIKRGIVKGKLSVNSAEERLKGSCPLMPQEIGI\n+LLRAYGYSKDAIIYVSGGEVFGGQRTLIPLHAMFENVIDRTSLSTPWEMI\n+RLYGKEVNLVDT-PGPPPFVE-EVTKRAAWKNAGPRPRPLPPPPARPK-S\n+YNIEGWWGWVAESDNEP----DSTVIELRTNAHKLLWEAIDYVICVEADV\n+FIPGFDRDGKGHPNFASLVMGHRLYQSAASKTFRPDRKEVAKLLDEICDH\n+RHH-ANHTWLETVRRHLTKTL-LDGIIEASNKSKPLSFLSHPVPECSCSR\n+RDS-FEVSKNS--SSPL-TSQLWTALSVAHQCPAWMDTGPISQSKDK---\n+ENEEDVDED-DSVSE-LFFK--Q-N-A----ENH---EGDAEVNIKEENQ\n+FEDQEDD-GGE-R\n+>29760.VIT_14s0083g00910.t01\n+-----MKGESKM-VFKSKMKWVGLVGLVLSAFSIFIHLLLARYTEDGISD\n+YQSSVTIFSWRPIFENADLP-RTSPLHRKFWGPVRRFEPLNPDANPRGYY\n+AAPPLQTNGYIFVRIQGGFHEIRNSISDVVVVSRLLNATLVIPEIQSTTS\n+SKGISSEFKSFAYLYNEDQFMIALAKDVKIVKTLPKNLKEARRKKEIPMF\n+RVPHSASPYFYLRNVLPVLNKHSVVELVVSDGGCLQAVLPPNLEEYQRLR\n+CRVAFHALRFRQEVQELATRILNRLRAPGRPFIAFDPGMTRDALAYHGCA\n+ELFQDVHTELIQHKRSWMIKRGIVKGKLSVDSAKQRLNGSCPLMPEEVGI\n+LLRAYGYSSDTIIYVSGGEVFGGQRTLIPLHGMFENVVDRTSLSTGWELN\n+RIYGLEVKIATNTPRIPTFVQ-EEMKLEAWKNSGPRPRPLPPPPARPKYP\n+YNIEGWWGWVAESDNEP----DRTVMELRTNAHKLLWEAIDYVICVEADV\n+FIPGFDRDGKGHPNFASLVMGHRLYQSAASITYRPDRKEVAKLLQETRDH\n+LYQ-ANRTWLTSVRMHLRKSL-FDGLTEASAKSKLLSFLSHPVPECSCLR\n+SNL-NEIPFPG--LSPPSQAQAQAALGAVHRCPAWIENALIPRQRDK---\n+DNDEDIDED-DSTSSGLFFR--P-RGG----NHE---VGGGEINNKEEAQ\n+LEDQEELEGAE-R\n+>3694.POPTR_0004s11200.1\n+-----MKGERKM-MIKSKMKWVGLVGLVLSAFSLFVHFLLARFTEEGITD\n+YQSSVTIFSWRPVFENPDFA-KNSPSYRRLWGPVRRLESLHPDANPRGYY\n+TDPRSESSGYVFVRIQGGFHEIRNSICDVVVISRLLNATLVIPEIQSTTR\n+SKGISSQFKSFAYLYNEDNFMAALVKDVKVVKTLPQNLKDARRLKKIPSF\n+RVPNSASPYFYLHHVLPVLNKHVVVELVVSDGGCLQAILPPQLEEYQRLR\n+CRVAFHALRFRQEVQELATKMLQRLRAPGQPFIAFDPGLTRDALAYYGCA\n+ELFQDVHNELIQHKRAWMKKRGIVKGKLSVNSAEQRLNGSCPLMPEEVGI\n+LLRAYGYPWDTILYVSGGEVFGGQRTLTPLHAMFENIVDRTSLSAAWELN\n+RIYGREVNLVDTKLRAPPSVV-QEKKHEVWKNEGPRPRPLPPPPARPKYP\n+YNIEGWWGWVAESDNEP----ESTVMELRTNAHKLLWEAIDYLICVEADV\n+FIPGFDRDGKGRPNFASLVMGHRLYQSAASKTFQPNRKEVVKLLEENREH\n+LYQ-ANHTWLTSTRSHLRRSL-IDGVMRASTESKPLSFLSHPVPECSCLR\n+SDL-TKRSLHT--SSPSTWAPVEAALGVMHHCPMWMDSGIKTKLKEK---\n+EIEEDPDED-ISSSSGLFFR--N-SGG----NHE---SGGGELIKEE--S\n+QLDDQEELEGA-D\n+>3694.POPTR_0017s13600.1\n+-----MKGEGKM-VIMSKMKWVGLVGLVLSAFSLFVHFLLARYTEEGISD\n+YQSSVTIFSWRPIFENSDFA-KNSPLYRRLWGQVRRLESLHPDANPRGYY\n+ADPRSESSGYVFVRIQGGFHEIRNSICDVVAISRLLNATLVIPEIQSTTS\n+SKGISSEFKSFAYLYNEDQFMAALVKDVKVVKTLPQNLKGARRKKKIPSF\n+RVPNSASPYFYLHHVLPVLNKHAVVELVVSEGGCLQAILPPHLEEYQRLR\n+CRVGFHALRFRQEVQELATKILHRLRAPGRPFIAFDPGMTRDALAYHGCA\n+ELFQDVHTELIQHKRAWMKKHGIVKGKLSVNSAKQRLNGSCPLMPEEVGI\n+LLRAYGYSWDTILYISGGEVFGGQRTLIPLHAMFENTVDRTSLSAAWEMS\n+RIYGREVNIVDTKLRAPPSVV-QEKKLEAWKNAGPRPHPLPPPPARPKYP\n+HNIEGWWGWVAESDNEP----ESTVMELRTNAHKLLWEAIDYLICVEADV\n+FIPGFDRDGKGRPNFASLVMGHRLYQSAASKTFRLDRKEVVKLLEENREH\n+LYQ-ANHTWLTSIRKHLRRSL-IDGVIEASSKSKPFSFLSHPAPECSCLR\n+YDP-TK--------------PVEASLGVMHSCPKWMDSEIKTKSKDK---\n+ETEEDSDED-VSSSSGLFFK--N-IGG----NNQ---SGGGELIKEE--S\n+QLDDQEELEGS-D\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.081.AA.strNOG.ENOG411BK9X.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.081.AA.strNOG.ENOG411BK9X.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,287 @@\n+>3218.PP1S184_96V6.1\n+--MVKVAFGEANEASSADALKGAFAEFLALFLFVFIGVGSVMSYEKIH-A\n+GDMDAAGLLVIAIAHGLAIAVLVSATANISGGHINPAVSLGLALAGKITV\n+IRLVLYWIAQLLGAAAGAWVLKIVTTGEDVARHAIGVGMTPWSAVLMEAV\n+LTFTLVFVVFATAVDPKKGTVGVIAPLAIGFTVLAQIFVGAPFSGASMNP\n+GRSFGPALVAMDFTNHWVYWVGPFIGAALAALIYDGVFISPS--PPPGHH\n+A-IPSDF--------\n+>3218.PP1S101_226V6.1\n+--MVKLAFGESDEASSPDALKGALAEFISLFLFVFIGVGSVMSYEKIH-V\n+GDLEAGGLLMIAIAHGLAIAILVAATANISGGHVNPAVSLGLALAGKITV\n+IRLVLYWVAQLLGAVAGAWVLKMVTTGEDVARHAIGVGMSPMSAVLMEIV\n+LTFTLVFVVFATAVDPKKGTVGVIAPLAIGFTVLAQIFVGAPFSGASMNP\n+GRSFGPAVIAMDFTNHWVYWVGPFIGAALAAVIYDGVFISPS--PPAGHQ\n+A-IPSDF--------\n+>3218.PP1S44_31V6.1\n+---MKIAFGEADEASSPDAIKGAVAEFISLFLFVFIGVGSVMAYEKIH-V\n+GDLDAAGLLMIAIAHGLAIAVLVAATANISGGHVNPAVSLGLALAGKITI\n+IRLVLYWVAQLLGAVAGAWVLKAVTTGEDVARHAIGANMTGFSAMLMEIV\n+LTFTLMFVVFATAVDPNKGTVGVIAPLAIGFTVLAQIFVGAPFSGASMNP\n+GRSFGPAVVAWDFKNHWVYWVGPLVGAALAALIYDGVFISPA--PPAGHQ\n+P-VPTEF--------\n+>3218.PP1S156_153V6.1\n+---MKVAFGEADEVSSPDALKGALAEFISLFLFVFIGVGSVMSYEKIH-V\n+GDLEAGGLLIIAIAHGLAIAILVAATANISGGHVNPAVSLGLALAGKITI\n+IRLVLYWIAQLLGAVAGAWVLKIVTTGEDLARHAIGAGMTTWSATLMEIV\n+LTFTLVFVVFATAVDPKKGTVGVIAPLAIGFTVLAQIFVGAPFSGASMNP\n+GRSFGPAVVAWDFTNHWVYWVGPFIGAALAALIYDGVFMSPA--APEGHQ\n+P-VPTEF--------\n+>29760.VIT_06s0061g00730.t01\n+MPFLRIAIGQPQETYQPDALKAALAEFFGTLIFVFAGEGSGMAFSKLTDD\n+GSTTPAGLIAEALGHGLGLFVAVSGACNISGGHINPAVTFGAFVGGNITL\n+LRGILYWIAQLLGSAVACLLLKFCTHGMTTSAFAISSGVTVWNAFVLEIV\n+MTFGLVYTVYATAIDPRKGNVGIIAPLAIGLIVAANILAGGAFDGASMNP\n+AMSFGPALVSWDWTNHWVYWAGPLIGGGIAGLVYETVFIHHTHEPLPGSE\n+F--------------\n+>88036.EFJ37418\n+--MARLTVGGADEYRQPDAMKAALAEFIGMFLFVFAGVGSAMAFAKLG-G\n+PILTPAGLVQIALAHGIALFVVIAATANISGGHINPAVTFGLAVGGHITI\n+ARGVLYWIAQLLGSVLAALVLKFTFLHEAVPIHAVGAHESVISALVIEIV\n+TTFALIFTVYGTAVDHKRGVVGTIAPIAIGFIVLANILAAGPFSGGSMNP\n+ARSFGPALVTFDWTNHWIYWVGPLIGGGLAGLVYNEILITPP----PPEE\n+Y--------------\n+>88036.EFJ33906\n+--MARLTVGGADEYRQPDAMKAALAEFIGMFLFVFAGVGSAMAFAKLG-G\n+PILTPAGLVQIALAHGIALFVVIAATANISGGHINPAVTFGLAVGGHITI\n+ARGVLYWIAQLLGSVLAALVLKFTFLHEAVPIHAVGAHESVISALVIEIV\n+TTFALIFTVYGTAVDHKRGVVGTIAPIAIGFIVLANILAAGPFSGGSMNP\n+ARSFGPALVTFDWTNHWIYWVGPLIGGGLAGLVYNEILITPP----PPEE\n+Y--------------\n+>88036.EFJ33577\n+--MARLAVGGADEYRQPDAMKGALAEFIGTFLFVFAGVGSAMAFAKLE-G\n+PILTPAGLVQIALAHGIALFVVIAATANISGGHINPAVTFGLAVGGHITI\n+ARGVLYWIAQLLGSVLAALVLKLTFLHESVPIHAVGAHESLISALVIEIV\n+TTFALIFTVYGTAVDHKRGVVGTIAPIAIGFIVLANILAAGPFSGGSMNP\n+ARSFGPALITFNWTNHWIYWVGPLIGGGLAGLVYNEILITPP----PPEE\n+Y--------------\n+>88036.EFJ36932\n+--MARLAVGGADEYRQPDAMKGALAEFIGTFLFVFAGVGSAMAFAKLE-G\n+PILTPAGLVQIALAHGIALFVVIAATANISGGHINPAVTFGLAVGGHITI\n+ARGVLYWIAQLLGSVLAALVLKLTFLHESVPIHAVGAHESLISALVIEIV\n+TTFALIFTVYGTAVDHKRGVVGTIAPIAIGFIVLANILAAGPFSGGSMNP\n+ARSFGPALITFNWTNHWIYWVGPLIGGGLAGLVYNEILITPP----PPEE\n+Y--------------\n+>3847.GLYMA11G03690.1\n+--MVKITLGTFDDSFGVASLKAYLAEFHATLIFVFAGVGSAIAYNELTKD\n+AALDPTGLVAVAVAHAFALFVGVSVAANISGGHLNPAVTFGLAIGGNITL\n+ITGFLYWIAQLLGSIVACLLLNFITA-KSIPSHAPATGVNDFQAVVFEIV\n+ITFGLVYTVYATAADPKKGSLGIIAPIAIGFVVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFAANWIYWVGPLIGGGLAGLIYGDVFIGS-YAAVPASE\n+T-YP-----------\n+>3847.GLYMA01G41670.1\n+--MVKIALGTLDDSFSAASLKAYFAEFHATLIFVFAGVGSAIAYNELTKD\n+AALDPTGLVAVAVAHAFALFVGVSVAANISGGHLNPAVTFGLAIGGNITL\n+ITGFLYWIAQLLGSIVACLLLNLITA-KSIPSHSPANGVNDLQAVVFEIV\n+ITFGLVYTVYATAVDPKKGSLGIIAPIAIGFVVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDLAANWIYWVGPLIGGGLAGLIYGDVFIGS-YAPVPASE\n+T-YP-----------\n+>4641.GSMUA_Achr11P21010_001\n+--MVKLALGSLGDSFSVVSLKSYLAEFIATLLFVFAGVGSAIAYGKLTGG\n+AALDPAGLVAVALAHGLALFVGVSMAANISGGHLNPAVTFGLAVGGHITI\n+LTGIFYWVAQLLGSTVACLLLKFVTGGLAVPTHGVAAGMSELEGVVMEVV\n+ITFALVYTVYATAADPKKGSLGTVAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVASGDFAGNWVYWVGPLIGGGLAGLIYGDIFIG-SYQPVAAQ-\n+D-YP-----------\n+>4641.GSMUA_Achr11P04570_001\n+--MVKLTLGSLGDSFSAGSLKAYLAEFIATLLFVFAGVGSAIAYGKLTSG\n+AALDPAGLVAVALAHGLALFVGVSMAANISGGHLNPAVTFGLAVGGHITL\n+LTGVFYWIAQLLGSTVACLLLKFVTGGMAVPTHGVAAGMSELEGVVMEVV\n+ITFALVYTVYATAADPKKGPLGTVAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVASGDFSGNWVYWVGPLIGGGLAGLIYGDIFIG-SYEAVAAQ-\n+D-YP-----------\n+>4558.Sb06g024590.1\n+--MVKLAFGSLGDSFSAASLKSYVAEFIATLLFVFAGVGSAIAYSQLTKG\n+GALDPAGLVAIAI'..b'NFAGNWVYWVGPLIGGGLAGLVYGDVFIG-SYQPVADQ-\n+D-YA-----------\n+>39946.BGIOSGA005904-PA\n+--MVKLAFGSLGDSFSATSVKAYVAEFIATLLFVFAGVGSAIAYGQLTNG\n+GALDPAGLVAIAIAHALALFVGVSVAANISGGHLNPAVTFGLAVGGHITI\n+LTGLFYWIAQLLGASIACLLLKFVTHGKAIPTHGVAG-ISELEGVVMEIV\n+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVAAGNFAGNWVYWVGPLIGGGLAGLVYGDVFIG-SYQPVADQ-\n+D-YA-----------\n+>4533.OB02G33850.1\n+--MVKLALGSLGDSFSAASVKAYVAEFIATLLFVFAGVGSAIAYGQLTNG\n+GALDPAGLVAIAIAHALALFVGVSVAANISGGHLNPAVTFGLAVGGHITI\n+LTGLFYWVAQLLGASVACLLLKFVTHGKAIPTHGVAG-ISELEGVVMEVV\n+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVAAGNFAGNWVYWVGPLVGGGLAGLVYGDVFIG-SYQPVADQ-\n+D-YA-----------\n+>29760.VIT_00s0229g00130.t01\n+--MVKLAFGSFGDSFSVGSLKAYLSEFNATLLFVFAGVGSAIAYGKLTSD\n+AALDPPGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGHITI\n+LTGIFYVIAQCLGSIVACLLLKFATNGESIPTHGVAAGMNAIEGVVMEIV\n+ITFALVYTVYATAVDPKKGSLGIIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFSENWIYWVGPLVGGGLAGLVYGNIFIES-YASVPISD\n+E-YA-----------\n+>3694.POPTR_0001s15700.1\n+--MVKIAFGSLGDSFSVGSLKAYLSEFIATLLFVFAGVGSAIAYSKLTTD\n+AALDPPGLVAVAVAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITI\n+LTGLLYWIAQCLGSIAACLLLKFATSAESIPTHGVASGMSAVEGVVMEIV\n+ITFALVYTVYATAADPKKGSIGIIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFSQNWIYWLGPLIGGGLAGLVYGDIFIGS-YTAAPVSE\n+D-YA-----------\n+>3694.POPTR_0003s07550.1\n+--MAKIAFGSLGDSFSLASIKAYLSEFIATLLFVFAGVGSAIAYSKLTTD\n+AALDPPGLVAVAVAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITF\n+LTGLLYWIAQCLGSIVACLLLKVVTSAEGIPTHGVASGMSAIEGVVMEIV\n+ITFALVYTVYATAADPKKGSLGIIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFSQNWIYWLGPLVGGGLAGLVYGGIFIGS-YAPAPVSE\n+D-YA-----------\n+>4081.Solyc06g060760.2.1\n+--MVKIAFGSIGDSLSVGSLKAYLAEFIATLLFVFAGVGSAIAFNKLTSG\n+AALDPAGLVAIAVAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITI\n+LTGLFYWVAQLLGSTVACLLLKYVTNGLAVPTHGVAAGMSGAEGVVMEIV\n+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVAGDFSQNWIYWVGPLIGGGLAGFIYGDVFIG-CHTPLPTSE\n+D-YA-----------\n+>4113.PGSC0003DMT400030994\n+--MVKIAFGSIGDSLSVGSLKAYLAEFIATLLFVFAGVGSAIAYNKLTSD\n+AALDPAGLVAIAVAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITI\n+LTGLFYWVAQLLGSTVACLLLKYVTNGLAVPTHGVAAGMSGAEGVVMEIV\n+ITFALVYTVYATAADPKKGSLGTIAPMAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVAGDFSQNWIYWVGPLIGGGLAGFIYGDVFIG-SHTPLPTSE\n+D-YA-----------\n+>3711.Bra024943.1-P\n+--MVKIAVASLGDSFSVASLKAYLPEFIATLIFVFAGVGSAIAFGKITSD\n+AALDPAGLVAIAVAHAFALFVGVSVAANISGGHLNPAVTLGLAVGGNITL\n+ITGFLYWVAQCLGSTVACLLLVFVTNGESVPTHGVGAGLGAVEAIVMEII\n+VTFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAIVSGDLSQIWIYWVGPLVGGALAGLIYGDVFIGSPYEAVETRE\n+I-RV-----------\n+>3702.AT5G47450.1\n+--MVKIEVGSVGDSFSVSSLKAYLSEFIATLLFVFAGVGSAVAFAKLTSD\n+GALDPAGLVAIAIAHAFALFVGVSIAANISGGHLNPAVTLGLAIGGNITL\n+ITGFFYWIAQCLGSIVACLLLVFVTNGKSVPTHGVSAGLGAVEGVVMEIV\n+VTFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDLSQIWIYWVGPLVGGALAGLIYGDVFIGS-YEAVETRE\n+I-RV-----------\n+>59689.fgenesh2_kg.8__49__AT5G47450.1\n+--MVKIELGSVGDSFSVSSLKAYLSEFIATLLFVFAGVGSAIAFDKLTSD\n+GALDPAGLVAIAIAHAFALFVGVSIAANISGGHLNPAVTLGLAIGGNITL\n+IIGFFYWIAQCLGSIVACLLLVFVTNGKSVPTHGVAAGLGAVEGIVMEIV\n+VTFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDLSQIWIYWVGPLVGGALAGLIYGDVFIGS-YEAVETRE\n+I-RV-----------\n+>59689.fgenesh2_kg.7__2576__AT4G17340.1\n+--MVKIEIGSLGDSFSVASLKAYLSEFIATLLFVFAGVGSALAFAKLTSD\n+AALDPAGLVAVAVAHAFALFVGVSIAANISGGHLNPAVTLGLAIGGNITV\n+ITGFFYWIAQCLGSIVACLLLVFVTNGESVPTHGVAAGLGAIEGVVMEIV\n+VTFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFSQIWIYWVGPLVGGALAGLIYGDVFIGS-YAPAPTTE\n+S-YP-----------\n+>3702.AT4G17340.1\n+--MVKIEIGSVGDSFSVASLKAYLSEFIATLLFVFAGVGSALAFAKLTSD\n+AALDPAGLVAVAVAHAFALFVGVSIAANISGGHLNPAVTLGLAVGGNITV\n+ITGFFYWIAQCLGSIVACLLLVFVTNGESVPTHGVAAGLGAIEGVVMEIV\n+VTFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFSQIWIYWVGPLVGGALAGLIYGDVFIGS-YAPAPTTE\n+S-YP-----------\n+>3711.Bra026245.1-P\n+--MVKIAIGSLGDSFSVASLKAYLSEFIATLLFVFAGVGSAIAFGKLTSN\n+AALDPAGLVAVAVAHAFALFVGVSIAANISGGHLNPAVTLGLAVGGNITV\n+ITGFFYWIAQCLGSIVACLLLAFVTNGESVPTHGVAAGLGAVEGIVMEIV\n+VTFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNP\n+ARSFGPAVVSGDFSQIWIYWVGPLVGGALAGLIYGDVFIGS-YAPAPTTE\n+S-YP-----------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.082.AA.strNOG.ENOG411BKC5.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.082.AA.strNOG.ENOG411BKC5.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,546 @@\n+>3711.Bra024926.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------MS-----ASSSSS-----T-NLVT-SE---\n+EA-NGGVTVLPGVEDKYGGVVTEI-SHPIDPSAFSALLRTSLSNWTLQGK\n+KGVWIKLPRHLIGLAETAVKEGFWFHHAEKDYLMLVYWI-PKD-DNTLPF\n+NASHRVSIAAFVINHKKEVLVVQEKTGRTKGKGIWKFPTGVVNEGEYIHD\n+GSVREVKEETGVDTEFVQVLAFRQTHKTFFEKSNLFFVCMLKPLSFEINA\n+QESEIEAAQWMPWEEYTKQPFVQNHELLRYMTDICSAK-TNGDYEGFTTI\n+P-------------------------------------------------\n+-----------------------VSE--HDQQ------------------\n+GNLYFNSRDLLPRH--------------------\n+>3711.Bra017472.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------MMI---SHMAKSHGL--IRL--LKKPCD-GC\n+LR---SPLFLRFPADGFSAFRS-YSL-TRSRFMS----T-DPIV-GE--E\n+AR-NGGVTMLPAVEDKYGGVMTEM-SRPMDPSAFSALLRSSLSNWTLQGK\n+KGVWIKLPRQLIGLAETAVKEGFWFHHAEKNYLMLVYWI-PKQ-DHTLPS\n+NASHRVGIAAFVLNHKKEVLVVQEKTGRFKGQGIWKFPTGVVNEGEYIHD\n+GSVREVKEETGVDTEFVQVLAFRQTHKAFFEKSDLFFVCMMKPLSLEINA\n+QESEIEAAQWMPWEEYNKQPFVQNHELLRYMTDICSAK-TNGDYEGFTPL\n+P-------------------------------------------------\n+-----------------------VSA--PDLQ------------------\n+GNLYFNNRDLSSRQ--------------------\n+>3711.Bra013893.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------MSD---H-ETPMVNGVV-EH--K\n+---I-GEEVLPFVEDEYGGVIVEMT-TPTDPKCFVATLRYSFTQWRSQGK\n+KGVWLNLPLSQVNLVEPAVKEGFRYHHAEPTYLMLVYWI-PES-ESTIPL\n+NASHRVRVGAVVLNHNKEILVVQEKYGLLRGSGVWKIPTGVVDEGEDIFA\n+AAIREVKEETGIDTEFLEVLAFCQTHESFFVKSDLFFICLLRPTSFDIQK\n+QDLEIEAAQWMPFEDSASQPITHKNELFKVIHRICSLK-MEKNYTGFSKK\n+P-------------------------------------------------\n+-----------------------TTTFFDDKL------------------\n+GYLYLNKQDMNNLIT-------------------\n+>3694.POPTR_0003s10530.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------MAF--SST-SSLPVMKQTK--P\n+-D--AERTLLNAVEDRYGGVKVDVE-DSMDCNDYVSLLRDSITQWRKQGK\n+KGVWIKLPIHLANLVEPTVKEGFRYHHAESDYLMLVYWI-PET-PDTLPA\n+NASHTVGIGAFVVNDNREVLVVQEKNGAFKGKDVWKFPTGVANQGEDICK\n+AAIREVKEETDIDTEFVEILAFSQTHQTFYGKSDLFFVCMLRPLSSDINK\n+QDSEIEAAQWMPIEEYVAQPFNQKHESFKNIANICLRK-SRRNYTGFSAV\n+P-------------------------------------------------\n+-----------------------MSSS-SGKK------------------\n+SYSYFNKLQLENETTN------------------\n+>3694.POPTR_0005s07920.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------MSSPPTS--V-L-KGQTALP-TD--K\n+-V--QQIGLLNAVNDKYGGVVVDMK-EPMDFHIYVPLLRASISQWRQQGK\n+KGVWIKLPIEQANLVEPTVKEGFRYHHAESNYLMLVYWI-PDS-PDTLPA\n+NASHIVGIGAFVMNNKRE-----EKHGYFKGKDAWKFPTGVVNQGEDICA\n+AAIREVKEETGIDTEFMEILAFNQTHQQFLGKSDLFFVCMLQPLSFDITK\n+QDSEIKAAQWIPIDEYVNQTYNREHKPFEYVAKICLTK-SQSNYGGFSAV\n+H-------------------------------------------------\n+-----------------------TLTS-SGKQ------------------\n+PYLYFNGQDFKP----------------------\n+>3847.GLYMA20G06680.1\n+M-------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------M-----\n+-----M------SSRASK-LVS-SS--LLAASKL--LLKSSSSAPPL-QT\n+TALVGSMVP----KVQG-PKH-SSGFPRSYM--SA--TLASLAK-EE--E\n+-VPSKGINTLRAIEDQHGGVIVNIE-NPMDSSVFSSLLEASISQWREQGK\n+KGVWIKLPREHSNLVDSAVKAGFRFHHAEPDYLMLVNWI-PNT-PDTLPA\n+NASHRVAVGAFVMNANREVLVVQESNGRFSGQGIWKLPTGGVDEGEDICT\n+AAVREVKEETGIDTKFVEVIAFKERHKSFFRKSELFFICMLQPHSFKIQR\n+QVSEIEAAQWMAIEDYMAQPFVRENELFDFLTKIGLSK-FNGKYSGFSTV\n+L---------------------'..b'--------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------MEKLVF-QN--G\n+---VKKDQLLSAVNDYHGGVIVELK-EPMDPNVFQNMLKASLSKWRLQGK\n+KGVWIKLPIELVNLVETAVKEGFWYHHAEPHYLMLVYWI-PET-ENTIPA\n+NASHRVGIGAIVLNDKRELLVVQENSGRLKGTAVWKIPTGIVEEGEDIFE\n+GAIREVKEETGIDTEFMEVLAFRQTHKVLFGKSDLFFICMMHPLSFDIQK\n+QDLEIEAAQWMPIEEYAALPFVQKHGLFKYIKDLCLVK-AERNYPGFTPV\n+P-------------------------------------------------\n+-----------------------ITSFFDAST------------------\n+SFLYCNKDGLDQESSASSSLKEDLEIETCKTILI\n+>29760.VIT_00s0259g00200.t01\n+M-------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------LRAL-----\n+-----L------PKPHIL-LFGPKFRAWKNLNPLP-NHHFLSTSFRY--P\n+LK---GVEVVGAVLGG--GVR-AMSGSAVSSA-S-A-AGEQLAS-GN--E\n+-VQQVTMKVLSAENDDHGGVIVEM-KEAMDFEAFVSLLRASIAHWRQQGK\n+RGVWIKMPIELVNLVEAAVKEGFWYHHAERKYLMLVYWI-PEG-PNTIPP\n+NATHRVGVGAFVLNEKGEMLVVQEKSGRFRGTGIWKFPTGVVDEGEDICD\n+AAVREVKEETGIDSKFVEVLAFR------------YVVCLT---------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------\n+>4113.PGSC0003DMT400021740\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------------MAK-EK--E\n+-M-VQVDRILAAKEDDYGGVTVEMTNEPLDPSVFASLLRASLSHWRQQGK\n+KGVWIKLPIELVMLVEPAVKEGFIYHHAEPKYLMLVSWL-PET-ANTIPA\n+NATHRVGIGAFVVNERNEVLVVQEKSGRFRGTGVWKFPTGVVDEGEDISD\n+AAVREVKEETGVNAKFVELLAFRQSHKSFFDKSDLFFVCMLQPLSHDIQM\n+QEREIEAAQWMPFEQYAAQPFVQGHDLLRYISDICSAK-MEGRYTGFSPV\n+P-------------------------------------------------\n+-----------------------TVTSFSAKK------------------\n+TYLYMNGNVRTTGQQRPLM---------------\n+>4081.Solyc05g054230.2.1\n+M-------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------I-----\n+-----I------KFICRS-TFL-SPRTSFFSS----KRHFFSCRPVK-LS\n+FC---QNQG-KLTKIRC-GII-NLNTRSSMS--C-S-ATPAMAK-EK--E\n+-M-EQVDKILAAKEDDYGGVTVEMTNEPLDPSVFASLLRASLSHWRQQGK\n+KGVWIKLPIELVMLVEPAVKEGFYYHHAEPKYLMLVSWL-PGT-ANTIPA\n+NATHRVGIGAFVVNERNEVLVVQEKSGRFRGTGVWKFPTGVVDEGEDISD\n+AAVREVKEETGVNAKFVELLAFRQSHKSFFDKSDLFFVCMLQPLSHDIQM\n+QEREIEAAQWMPFEQYAAQPFVQGHDLLRYISDICSAK-MEGRYTGFSPV\n+P-------------------------------------------------\n+-----------------------TVTGFSAKK------------------\n+TYLYMHGNVRTTGSSNDP----------------\n+>3218.PP1S38_200V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------M-AR----SS--S-F--PCQLDT---LMN\n+---DQPVQTLISAEDKYGGLVIDVESLPTNTSVFVDSLNHSLAQWRTQGK\n+KAVWLKLTIENSYLVDPAIKAGFIYHHAEPTHVMLVTWL-SKE-QSTVPA\n+NASHQVGIGAFILNDKQEILAVQERSGVFQGAGIWKMPTGSVNQGEDIFS\n+GAIREVKEETGVDTEFVDVIGFRQSHAAAFGKSDIFFLCVLRPVTSEITV\n+QDSELTAVKWMPIAEFKDQTYLKQRKLLKKMLEVCLATTTESGYKGFKIE\n+D-------------------------------------------------\n+-----------------------VQAGTGRRP------------------\n+QYFFYNADDCKE----------------------\n+>3218.PP1S14_281V6.2\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------------MVCISFCNRCS-----RIIAVSSRW\n+FESLAG------SRAAAG-RIS-YS--VIRVSRI--SAWSSKSAGHL-QT\n+NA---SGFRQVLRMDG--DTSK-DLSTGVAL--P-P-PDDEFVS-EKELE\n+---SWTNTILPGQYDSYEGVIIDHRSLPSDASVFKKYLIASIAQWKKERK\n+HGIWLKLPIENVKLVEAAVAAGFGYHHAEPAYLMLTLWL-PDG-PCTLPP\n+NASHQVGVGAFVLNDKNEILAVQEKNGPLKGTGVWKMPTGLTNQGEDIFD\n+GAIREVKEETGVDARFVEVVGFRQGHQCQFDKSDLFFLCILRPTSTEIVA\n+QESEIAAAKWMPLSEFKAQPIFDTRPTMKKMLEVCLAR-VEGKYQGFAYE\n+D-------------------------------------------------\n+-----------------------IHPDSLNSN------------------\n+SYFYYNQVDFFGSQQQSIFRAKDGERSCRRVV-T\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.083.AA.strNOG.ENOG411BMKC.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.083.AA.strNOG.ENOG411BMKC.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,297 @@\n+>88036.EFJ25658\n+MDC-----------------------------------------KKALIT\n+GITGQDGSYLTEFLLSKGYEVHGIIRRSSNFNTQRLDHIYIDPH---I-S\n+AARMKLHYGDLADASALRKWVDAILPDEVYNLGAQSHVGVSFENPDYTAD\n+VVATGALRLLEAVKTHCSTTGRQ-IRYYQAGSSEMYGSTPPPQDEATAFH\n+PRSPYAAAKVAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQKKLFLGNLKASRDWGFAGDYVQAMWLMLQQETPDDYVVA\n+TEESHTVEEFLEEAFGYVGLEWREHVEIDPRYFRPTEVDNLRGSAAKARS\n+ALGWKPKVSFKQLVAMMVDSDLEKAQREKVLVEHGFIDSHQQP\n+>88036.EFJ22289\n+MDC-----------------------------------------KKALIT\n+GITGQDGSYLTEFLLSKGYEVHGIIRRSSNFNTQRLDHIYIDPH---I-S\n+AARMKLHYGDLADASALRKWVDAILPDEVYNLGAQSHVGVSFENPDYTAD\n+VVATGALRLLEAVKTHCATTGRQ-IRYYQAGSSEMYGSTPPPQDEATAFH\n+PRSPYAAAKVAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQKKLFLGNLKASRDWGFAGDYVQAMWLMLQQETPDDYVVA\n+TEESHTVEEFLEEAFGYVGLEWREHVEIDPRYFRPTEVDNLRGSAAKARS\n+ALGWKPKVSFKQLVAMMVDSDLEKAQREKVLVEHGFIDSHQQP\n+>3218.PP1S444_21V6.1\n+MSQEA------AA---S---------------------------KRALIT\n+GITGQDGSYLTEFLLKKGYEVHGIIRRSSNFNTQRLEHIYIDPH---Q-S\n+SARMKLHYGDLSDASSLRKWVDSIRPDEVYNLGAQSHVGVSFENPDYTAD\n+VVGTGTLRLLEAIRIHIQATGRL-VKYYQAGSSEMYGATPPPQDETTVFH\n+PRSPYAVAKVAGHFYTVNYREAYGMFACNGILFNHESPRRGENFVTRKIT\n+RAIGRIKVGLQKKLYLGNLKASRDWGFAGDYVEGMWMMLQQEKPDDYVLA\n+TEDSHTVEEFLEEAFSYVGLNWKDHVEIDPRYFRPSEVDNLRGSAQKAKE\n+VLGWQPKVQFKQLVAMMVDGDLEKAKREKVLVDAGFIDSHQQP\n+>3218.PP1S177_34V6.1\n+MAHKPT---AFTD---LVSM--------------APENA---PLKKALIT\n+GITGQDGSYLTEFLLKKGYEVHGIIRRSSNFNTQRLEHIYIDPH---N-S\n+SARMKLHYGDLSDASSLRKWVDTICPDEVYNLGAQSHVGVSFENPDYTAD\n+VVATGALRLLEAVRIHVESTGRL-VKYYQAGSSEMYGATPPPQDETTVFH\n+PRSPYAVAKVAAHFYTVNYREAYGLFACNGILFNHESPRRGENFVTRKIT\n+RAIGRIKIGLQKKLFLGNLKASRDWGFAGDYVEGMWLMLQQDKPDDYVLA\n+TENSYTVEEFLEEAFGYVGLNWKDHVEIDPRYFRPSEVDNLRGSAQKARE\n+LLGWQPKVNFKQLVAMMVDSDLERAKREKVLVDNGYIDSHQQP\n+>3218.PP1S169_107V6.1\n+MAHKPT---AFSD---LVAM--------------APGDA---PLKKALIT\n+GITGQDGSYLTEFLLKKGYEVHGIIRRSSNFNTQRLEHIYIDPH---N-S\n+SARMKLHYGDLSDASSLRKWVDTICPDEVYNLGAQSHVGVSFENPDYTAD\n+VVATGALRLLEAVRIHVQSTGRQ-VKYYQAGSSEMYGATPPPQDETTVFH\n+PRSPYAVAKVAAHFYTVNYREAYGLFACNGILFNHESPRRGENFVTRKIT\n+RAIGRIKIGLQKKLFLGNLKASRDWGFAGDYVEGMWLMLQQEKPDDYVLA\n+TESSYTVEEFLEEAFGYVGLNWRDHVEIDPRYFRPSEVDNLRGSAQKARE\n+RLGWQPKVNFKQLVAMMVDGDLERAKREKVLVDNGYIDSHQQP\n+>4113.PGSC0003DMT400009345\n+MAAENG---STG---N-S--------------------P---RSKIALIT\n+GITGQDGSYLTELLISKNYEVHGLIRRSSSFNTQRINHIYIDPH---NTY\n+RAKMKLHYADLSDASSLRRWLDIILPDEIYNLAAQSHVAVSFEIPDYTAD\n+VVATGALRLLEALRSHISATGRSHVKYYQAGSSEMFGSTPPPQSESTPFH\n+PRSPYAVSKCSAHWYTVNYREAYGIFACNGILFNHESPRRGENFVTRKIT\n+RAVGRIKIGLQSKVFLGNLQASRDWGFAGDYVEAMWMMLQQEKPDDYVVA\n+TEDSHTVEEFLEVAFRYVGLNWKEHVEIDKRYFRPTEVDNLKGDASKATK\n+VLGWKPKVGFEQLVKMMVDEDVELAKREKVLVDAGYIDAQQQP\n+>4081.Solyc02g084210.1.1\n+MAAENG---STG---NKN--------------------G---RSKIALIT\n+GITGQDGSYLTELLISKNYQVHGLIRRSSSFNTQRINHIYIDPH---NTC\n+RAKMKLHYADLSDASSLRRWLDIILPDEIYNLAAQSHVAVSFEIPDYTAD\n+VVATGALRLLEALRSHISATGRSHVKYYQAGSSEMFGSTPPPQSETTPFH\n+PRSPYAVSKCSAHWYTVNYREAYGIFACNGILFNHESPRRGENFVTRKIT\n+RAVGRIKIGLQSKVFLGNLQASRDWGFAGDYVEAMWMMLQQEKPDDYVVA\n+TEDSHTVEEFLEVAFGYVGLNWKEHVEIDKRYFRPTEVDNLKGDASKAKK\n+VLGWKPKVGFEQLVKMMVDEDVELAKREKVLVDAGYIDAQQQP\n+>59689.scaffold_502169.1\n+MASENN---GPR---SESESITKADS--TVVE-----MPPSQPRKIALIT\n+GITGQDGSYLTEFLLGKGYEVHGLIRRSSNFNTQRLNHIYIDPH---NVN\n+KALMKLHYADLTDASSLRRWLDVIKPDEVYNLAAQSHVAVSFEIPDYTAD\n+VVATGALRLLEAVRSHTIDSGRT-VKYYQAGSSEMFGSTPPPQSETTPFH\n+PRSPYAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKIT\n+RALGRIKVGLQTKLFLGNLQASRDWGFAGDYVEAMWLMLQQEKPDDYVVA\n+TEEAHTVEEFLDVSFGYLGLDWKNHVEIDPRYFRPSEVDNLQGDASKAKE\n+VLGWKPKVGFETLVKMMVDEDLALANREKLLVDAGYMDAKQQP\n+>3702.AT3G51160.1\n+MASENN---GSR---SDSESITAPKA--DSTV-----VE---PRKIALIT\n+GITGQDGSYLTEFLLGKGYEVHGLIRRSSNFNTQRINHIYIDPH---NVN\n+KALMKLHYADLTDASSLRRWIDVIKPDEVYNLAAQSHVAVSFEIPDYTAD\n+VVATGALRLLEAVRSHTIDSGRT-VKYYQAGSSEMFGSTPPPQSETTPFH\n+PRSPYAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKIT\n+RALGRIKVGLQTKLFLGNLQASRDWGFAGDYVEAMWLMLQQEKPDDYVVA\n+TEEGHTVEEFLDVSFGYLGLNWKDYVEIDQRYFRPAEVDNLQGDASKAKE\n+VLGWKPQVGFEKLVKMMVDEDLELAKREKVLVDAGYMDAKQQP\n+>3711.Bra038888.1-P\n+MASENN---GST---AV-ET----------------------PRKVALVT\n+GITGQDGSYLTELLLEKGYEVHGLIR'..b'EAMWMMLQQDEPGDYVVA\n+TEESHTVEEFLQAAFGHVGLDWKDHVVIDPKYFRPAEVDSLKGDSTKARK\n+ALGWKPKVGFQDLVKMMVDHDLEIAKREKVLVDAGYIDAQQQP\n+>4538.ORGLA06G0024100.1\n+MATTQHSNGGAA---GDNG---E--A--APPSVPPSLAP---PRKVALVT\n+GITGQDGSYLTELLLGKGYEVHGLIRRSSNFNTQRLDHIYHDPHSQPSTP\n+RPPMRLHYADLSDSSSLRRALDHILPDEVYNLAAQSHVAVSFEVPDYTAD\n+VTATGALRLLEAVRLA-----SKRIRYYQAGSSEMFGSTPPPQSESSPFH\n+PRSPYAAAKVAAHWYTVNYREAYGLFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLSAARDWGFAGDYVEAMWRMLQQDKPGDYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLQGDATKARK\n+ELGWKPKIGFQQLVEMMVDNDIELAKKEKVLVDAGYRDPKQQP\n+>39946.BGIOSGA022260-PA\n+MATTQHSNGGAA---GDNG---E--A--APPSVPPSLAP---PRKVALVT\n+GITGQDGSYLTELLLGKGYEVHGLIRRSSNFNTQRLDHIYHDPHSQPSTP\n+RPPMRLHYADLSDSSSLRRALDHILPDEVYNLAAQSHVAVSFEVPDYTAD\n+VTATGALRLLEAVRLA-----SKRIRYYQAGSSEMFGSTPPPQSESSPFH\n+PRSPYAAAKVAAHWYTVNYREAYGLFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLSAARDWGFAGDYVEAMWRMLQQDKPGDYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLQGDATKARK\n+ELGWKPKVGFQQLVEMMVDNDIELAKKEKVLVDAGYRDPKQQP\n+>39947.LOC_Os06g04620.1\n+MATTQHSNGGAA---GDNG---E--A--APPSVPPSLAP---PRKVALVT\n+GITGQDGSYLTELLLGKGYEVHGLIRRSSNFNTQRLDHIYHDPHSQPSTP\n+RPPMRLHYADLSDSSSLRRALDHILPDEVYNLAAQSHVAVSFEVPDYTAD\n+VTATGALRLLEAVRLA-----SKRIRYYQAGSSEMFGSTPPPQSESSPFH\n+PRSPYAAAKVAAHWYTVNYREAYGLFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLSAARDWGFAGDYVEAMWRMLQQDKPGDYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLQGDATKARK\n+ELGWKPKVGFQQLVEMMVDNDIELAKKEKVLVDAGYRDPKQQP\n+>4555.Si006699m\n+MAH---SNGEATAAG-----------DGEVAPVPRPLAP---PRKVALIT\n+GITGQDGSYLTELLLSKGYEVHGLIRRSSNFNTQRLDHIYHDPHAVPSSP\n+RPAMRLHYADLSDSSSLRRALDAISPDEVYNLAAQSHVAVSFEIPDYTAD\n+VTATGALRLLEAVRLA-----RKPIRYYQAGSSEMFGSTPPPQSEDTPFH\n+PRSPYAAAKVAAHWYTVNYREAYGLFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLTAARDWGFAGDYVEAMWLMLQQDQPGDYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLKGDSTKARR\n+ELKWKPKVGFQQLVEMMVDHDIELANKEKVLVDAGYRDPKQQP\n+>4577.GRMZM2G115124_P01\n+MAH---STTATATAT-----------DGETAPVPRALAP---ARKVALIT\n+GITGQDGSYLTELLLSKGYEVHGLMRRSSNFNTQRLDHIYHDPHAVPSSP\n+RPPLRLHYADLSDSSSLRRALDAISPDEVYNLAAQSHVAVSFEVPDYTAD\n+VTATGALRLLEAVRLS-----RRPIRYYQAGSSEMFGSTPPPQGEDTPFH\n+PRSPYAAAKVAAHWYTVNYREAYGVFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKLGLQTKVFLGNLSAARDWGFAGDYVEAMWLMLQQDQPADYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLQGDSTKARK\n+LLKWKPKVGFQQLVEMMVDRDVELAKKEKVLVDAGYRDPKQQP\n+>4558.Sb10g002550.1\n+MAH---SNGAAATATAA--------GDGETTPVPRPLAP---AQKVALIT\n+GITGQDGSYLTELLLSKGYEVHGLIRRSSNFNTQRLDHIYHDPHAVPSSP\n+RPLMQLHYADLTDSSSLRRVLDAVSPDEVYNLAAQSHVAVSFEVPDYTAD\n+VTATGALSLLEAVRLS-----RKPIRYYQAGSSEMFGSTPPPQSEDTPFH\n+PRSPYAASKVAAHWYTVNYREAYGIFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKLGLQTKVFLGNLSAARDWGFAGDYVEAMWLMLQQDQPADYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLKGDSTKARK\n+VLKWKPKVGFQQLVEMMVDHDIELAKKEKVLVDAGYRDPKQQP\n+>4558.Sb10g002560.1\n+MAH---SNGAAATATAA--------GDGETAPVPRSLAP---ARKVALIT\n+GITGQDGSYLTELLLSKGYEVHGLIRRSSNFNTQRLDHIYHDPHAVPSSP\n+RPPMRLHYADLSDSSSLRRALDAIAPDEVYNLAAQSHVAVSFEVPDYTAD\n+VTATGALRLLEAVRLS-----RKPIRYYQAGSSEMFGSTPPPQSEDTPFH\n+PRSPYAAAKVAAHWYTVNYREAYGIFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLSAARDWGFAGDYVEAMWLMLQQDQPADYVVA\n+TEESHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPAEVDSLKGDSTKARK\n+VLKWKPKVGFQQLVEMMVDHDIELAKKEKVLVDAGYRDPKQQP\n+>4513.MLOC_73895.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------------MFGSTPPPQSEATPFH\n+PRSPYAVAKVAAHWYTVNYREAYGLFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLSAARDWGFAGDYVEAMWLMLQQDKPDDYVVA\n+TEECHTVEEFLQAAFGYAGLNWKDHVVIDKKYFRPSEVDCLEGDSSKSRR\n+VLGWKPKVGFQQLVEMMVDKDIELAMKEKVLVDAGYRDT----\n+>15368.BRADI1G51460.1\n+MA-APHSNGGAA---AGAG--EEEAV--AVASVPRSLAP---PRKVALVT\n+GITGQDGSYLTELLLSKGYEVHGLIRRSSNFNTQRLDHLYHDPHATPSAA\n+RPPMRLHYADLSDSSSLRRALDHVLPDEVYNLAAQSHVAVSFEIPDYTAD\n+VTATGALRLLEAVRLS-----AKPMRYYQAGSSEMFGSTPPPQSEDTPFH\n+PRSPYAAAKVAAHWYTVNYREAYGIFACNGVLFNHESPRRGENFVTRKIT\n+RAVGRIKVGLQTKVFLGNLSAARDWGFAGDYVEAMWLMLQQDKPGDYVVA\n+TEECHTVEEFLQAAFGYAGLDWKDHVVIDKKYFRPAEVDCLKGDSSKSRR\n+ELGWKPKVGFQQLVEMMVDNDIELAKKEKVLVDAGYRDPKQQP\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.084.AA.strNOG.ENOG411BNP9.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.084.AA.strNOG.ENOG411BNP9.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,231 @@\n+>88036.EFJ12888\n+----------------------------------MLTPQQRLQLDESRWR\n+LHSVLSAAQP---------H-QCANLLLQRIDAPVSAVWPMLRRFDTPQA\n+YKRFVKACVIASGDGSSVGSLRNITLISGLPASCSTERLEILDDEHHIVS\n+FRVVGGEHRLRNYASVTSLHE-----------------------KVVTVV\n+MESYVVDVPEGNTREDTRVFTDTVVRCNLQSLAKICQANF-KLEQRRCQQ\n+QQQQQPEMASCKKDSGQDSGLILMR\n+>88036.EFJ17082\n+--------------------------------------------------\n+---------P---------H-QCANLLLQRIDAPVSAVWPMLRRFDTPQA\n+YKRFVKACVIASGDGSSVGSLRNITLISGLPASCSTERLEILDDEHHIVS\n+FRVVGGEHRLRNYASVTSLHE-----------------------KVVTVV\n+MESYVVDVPEGNTREDTRVFTDTVVRCNLQSLAKICQ-------------\n+-------------------------\n+>3711.Bra007772.1-P\n+-------------------------MSSSPVVK-GLTDEEHKTLE-PVIN\n+TYHQFEP-DP---------T-TCTSLVAQRIDAPASVVWPLIRSFDNPQR\n+YKHFVKSCRRVSGDGG-VGSVREVTVISGIPASTSTERLEFLDDDHRVLS\n+FRVVGGEHRLNNYKSVTSVNEFLNQD----------------SGRVYTVV\n+LESYTVDVPEGNTVEDTRMFVDTVVKLNLQKLGVIATAAPTH--------\n+--------------------D----\n+>3702.AT2G26040.1\n+-------------------------MSSSPAVK-GLTDEEQKTLE-PVIK\n+TYHQFEP-DP---------T-TCTSLITQRIHAPASVVWPLIRRFDNPER\n+YKHFVKRCRLISGDGD-VGSVREVTVISGLPASTSTERLEFVDDDHRVLS\n+FRVVGGEHRLKNYKSVTSVNEFLNQD----------------SGKVYTVV\n+LESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDD------\n+--------------------E----\n+>59689.scaffold_400801.1\n+-------------------------MSSSPVVK-GLTDEEHKTLE-PVIK\n+TYHRFEP-DP---------S-TCTSLITQRIDAPASSVWPLIRRFDNPER\n+YKHFVKSCRLISGDGG-IGSVREVTVISGLPASTSTERLEFVDDDHRVLS\n+FRVVGGEHRLKNYKSVTSVNEFLNQD----------------SGKVYTVV\n+LESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD-------\n+--------------------E----\n+>29760.VIT_04s0008g00890.t01\n+MD----------------------PHHH----H-GLTEEEFRALE-PIIQ\n+NYHTFEP-SP---------N-TCTSLITQKIDAPAQVVWPFVRSFENPQK\n+YKHFIKDCTM-RGDGG-VGSIREVTVVSGLPASTSTERLEILDDEKHILS\n+FRVVGGEHRLNNYRSVTSVNDFSK------------------EGKDYTIV\n+LESYIVDIPEGNTGEDTKMFVDTVVKLNLQKLAVVAITSL-HEN------\n+--------------------E----\n+>3694.POPTR_0006s24670.1\n+MD----------------------ANHAPPVPQ-GLTQEEYVELK-PLID\n+TYHKFGAAVP---------N-TCTSLITQRIDAPAHVVWPFVRRFDNPQK\n+YKHFIKSCKMSAGDGG-VGSIREVTVVSGIPASTSTERLEILDDENHILS\n+FRVVGGEHRLNNYKSVTSVNEFNK------------------EDKVYTIV\n+LESYIVDIPDGNTVEDTEMFVDTVVKLNLQKLAVVANTAL-HGH------\n+--------------------E----\n+>3694.POPTR_0018s05090.1\n+MD----------------------TNQAPP-PQ-GLTQEEYMELK-PLID\n+TYHKFEP-AP---------N-TCTSLITQRIDAPAHVVWPFVRRFDNPQK\n+YKHFIKSCNMSAGDGG-VGSVREVAVVSGLPASTSIERLEILDDENHILS\n+FRVVGGEHRLNNYKSVTSVNEFNK------------------EGKVYAIV\n+LESYIVDIPGGNTGEDTKMFVDTVVKLNLQKLAVVAIASL-HGH------\n+--------------------E----\n+>4113.PGSC0003DMT400077008\n+-M----------------------ARTNCQVPQ-GLKQEEFIELE-PLIR\n+NYHTFEH-LS---------N-TCTSLITQRIEAPANVVWPFVRRFDNPQK\n+YKHFIKSCKM-TGDGG-VGSIREVSVVSGIPASTSTERLEILDDEKHILS\n+FRVVGGEHRLNNYKSVTSVNGFEK------------------NGKAYTIV\n+LESYIVDIPQGNTGEDTKMFTDTVVKLNLQKLGVVAMAAM-HGH------\n+--------------------E----\n+>4081.Solyc12g095970.1.1\n+MD----------------------GDRQLLVPQ-GLTQEEFVELE-PLIR\n+NYHTFED-LP---------N-TCTSLVTQRIDAPVDVVWPFIRRFDNPEK\n+YKHFIKSCRIVSGDGG-VGSIREVTVVSGIPASTSTERLEILDDEKHILS\n+FRVVGGEHRLTNYKSVTSVNEFKK------------------NGKIYTIV\n+LESYIVDIPEGNTGEDTKMFTDTVVKLNLQKLALVAMSTM-HGH------\n+--------------------E----\n+>4113.PGSC0003DMT400075340\n+MD----------------------GDGQLLVPQ-GLTQEEFAELE-PLIR\n+NYHTFED-LP---------N-TCTSLVTQRIDAPVDVVWPFVRRFDNPEK\n+YKHFIKSCRIVSGDGG-VGSIREVTVVSGIPASTSTERLEILDDEKHILS\n+FRVVGGEHRLTNYKSVTSVNEFSK------------------NGKNYTIV\n+LESYIVDIPEGNTGEDTKMFTDTVVKLNLQKLALVAMSAM-HGH------\n+--------------------E----\n+>3847.GLYMA06G05440.1\n+----------------------MASEAYDP-VL-GLTPEEFTELE-STIN\n+THHKFEA-SP---------E-ICSSIIAQRIDAPAHTVWPLVRSFENPQK\n+YKHFVKSCNMRSGDGG-VGSIREVTVVSGLPASTSTERLEILDDDNHLLS\n+FRVVGGEHRLHNYRSVTSVNEFKRPD----------------NGKVYTIV\n+LESYVVDIPEGNTGVDTKMFVDTVVKLNLQKLGEVAMATN----------\n+-------------------------\n+>3847.GLYMA04G05380.1\n+----------------------MASEAYPV-L--GLTPEEFSELE-SIIN\n+THHKFEP-SP---------E-ICSSIIAQRIDAPAHTVWPLVRSFENPQK\n+YKHFVKSCNMRSGDGG-VGSIREVTVVSGLPASTSTERLEILDDDKHLLS\n+FRVVGGEHRLHNYRSVTSVNEFKNPD----------------NGKVYTIV\n+LESYVVDIPEGNTGVDTK'..b'-PA\n+----------------------MEAHVERALRE-GLTEEERAALE-PAVM\n+AHHTFPPSTT----TATTAAATCTSLVTQRVAAPVRAVWPIVRSFGNPQR\n+YKHFVRTCALAAGDGASVGSVREVTVVSGLPASTSTERLEMLDDDRHIIS\n+FRVVGGQHRLRNYRSVTSVTEFQPPA------------AGPGPAPPYCVV\n+VESYVVDVPDGNTAEDTRMFTDTVVKLNLQMLAAVAEDSSS-ASRRR--D\n+-------------------------\n+>39947.LOC_Os06g36670.1\n+----------------------MEAHVERALRE-GLTEEERAALE-PAVM\n+AHHTFPPSTT----TATTAAATCTSLVTQRVAAPVRAVWPIVRSFGNPQR\n+YKHFVRTCALAAGDGASVGSVREVTVVSGLPASTSTERLEMLDDDRHIIS\n+FRVVGGQHRLRNYRSVTSVTEFQPPA------------AGPGPAPPYCVV\n+VESYVVDVPDGNTAEDTRMFTDTVVKLNLQMLAAVAEDSSS-ASRRR--D\n+-------------------------\n+>4533.OB06G26150.1\n+----------------------MEAHVERALRE-GLTEEERAALE-PAVL\n+AHHTFPGRAAAPAEGAAAATATATSLVTQHVAAPLRAVWPIVRSFGNPQR\n+YKHFVRTCALAEGDGASVGSVREVAVVSGLPASTSTERLEILDDDRHIIS\n+FRVLGGQHRLRNYRSVTSVTEFQPQ---------------PGAPSPYCVV\n+VESYVVDVPDGNTEDDTRMFTDTVVKLNLQKLAAVAEESAA-SSASRRRD\n+-------------------------\n+>4555.Si008300m\n+----------------------MEAHVERALRA-TLTEAEARALE-GTVH\n+EHHTFPGRSRAG-AGAAAAAATCTSLVAQRVSAPVRCVWPIVRSFGNPQR\n+YKHFVRTCALAAGDGASVGSVREVTVVSGLPASSSTERLEVLDDDRHILS\n+FRVVGGDHRLRNYRSVTSVTEFQRQH--------------PAGGPPYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVRLNLQRLAAVAEESAG-GGR----S\n+-------------------------\n+>4558.Sb10g022200.1\n+----------------------METHVERALRA-TLTEAEVRALE-PAVR\n+EHHTFPAGRVAA-GTTTPTPTTCTSLVAQRVSAPVRAVWPIVRSFGNPQR\n+YKHFVRTCALAAGDGASVGSVREVTVVSGLPASSSTERLEVLDDDRHILS\n+FRVVGGDHRLRNYRSVTSVTEFQ--------------------PGPYCVV\n+VESYAVDVPEGNTAEDTRMFTDTVVRLNLQKLAAVAEESAA-AAAAGNRR\n+-------------------------\n+>15368.BRADI3G08580.1\n+----------------------MEPHMERALRE-ALTEAERRSLA-PVVA\n+AHHTFPGSGQSSPSPSPGKKKTCTSLVTQRVDAPLAAVWAIVRGFATPQR\n+YKHFIKSCALAAGDGATVGSVREVTVVSGLPASTSTERLEILDDDRHVLS\n+FRVVGGEHRLRNYRSVTSVTEFSSPPPPEPEEKEKEETQDAAASSSYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAIATTSTS-SPSASPSS\n+PPPPQPS-----------DGAQADH\n+>4513.MLOC_39291.1\n+----------------------MEHHMESALRQ-GLTEPERRELE-GVVE\n+EHHTFPGRA---------SG-TCTSLVTQRVQAPLAAVWDIVRGFANPQR\n+YKHFIKSCALAAGDGATVGSVREVTVVSGLPASTSTERLEILDDDRHILS\n+FCVVGGEHRLRNYRSVTSVTEFTDQP----------------SGPSYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAIATTTSS-PPPLDGQS\n+-------------------------\n+>4538.ORGLA02G0084300.1\n+----------------------MEPHMERALREAVASEEERRELE-GVVR\n+AHHTFPAAERA---AGPWRRPTCTSLVAQRVDAPLAAVWPIVRGFANPQR\n+YKHFIKSCELAAGDGATVGSVREVAVVSGLPASTSTERLEILDDDRHVLS\n+FRVVGGDHRLRNYRSVTSVTEFSSPS------------SPPSPSRPYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAVATSSSP-PAA-----\n+---GNHH------------------\n+>39946.BGIOSGA006847-PA\n+----------------------MEPHMERALREAVASEAERRELE-GVVR\n+AHHTFPAAERA---AGPGRRPTCTSLVAQRVDAPLAAVWPIVRGFANPQR\n+YKHFIKSCELAAGDGATVGSVREVAVVSGLPASTSTERLEILDDDRHVLS\n+FRVVGGDHRLRNYRSVTSVTEFSSPS------------SPPSPPRPYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAVATSSSP-PAA-----\n+---GNHH------------------\n+>39947.LOC_Os02g13330.1\n+----------------------MEPHMERALREAVASEAERRELE-GVVR\n+AHHTFPAAERA---AGPGRRPTCTSLVAQRVDAPLAAVWPIVRGFANPQR\n+YKHFIKSCELAAGDGATVGSVREVAVVSGLPASTSTERLEILDDDRHVLS\n+FRVVGGDHRLRNYRSVTSVTEFSSPS---------------SPPRPYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAVATSSSP-PAA-----\n+---GNHH------------------\n+>4558.Sb04g008040.1\n+----------------------MEPHMETALRQGGLSELEQRELE-PVVR\n+AHHTFPGRS---------PGTTCTSLVTQRVDAPLSAVWPIVRGFAAPQR\n+YKHFIKSCDLRSGDGATVGSVREVTVVSGLPASTSTERLEILDDDRHILS\n+FRVVGGDHRLRNYRSVTSVTEFHHHH------------Q-AAAGRPYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAIATSSAA-AAA-----\n+---SNSS-----------T------\n+>4577.GRMZM2G154987_P01\n+----------------------MEPHMESALRQ-GLSEAEQRELE-GVVR\n+AHHTFPGRA---------PG-TCTSLVTQRVDAPLAAVWPIVRGFGSPQR\n+YKHFIKSCDLKAGDGATVGSVREVTVVSGLPASTSTERLEILDDHRHILS\n+FRVVGGDHRLRNYRSVTSVTEFQP--------------------GPYCVV\n+LESYVVDVPDGNTEEDTRMFTDTVVKLNLQKLAAIATSSSA-N-------\n+-------------------------\n+>4555.Si018378m\n+----------------------MEPHMEGALRQ-GLSEAEQRELE-SVVR\n+AHHTFPGRA---------PG-TCTSLVTQRVDAPLAAVWPIVRGFASPQR\n+YKHFIKSCDLRSGDGATVGSVREVTVVSGLPASTSTERLEILDDDRHILS\n+FRVVGGDHRLRNYRSVTSVTEFQP--------------------GPYCVV\n+VESYVVDVPEGNTEEDTRMFTDTVVKLNLQKLAAIATSSSS-SPR-----\n+---PSGG-----------GGGGTDH\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,248 @@\n+>88036.EFJ07870\n+--------------------------------------------------\n+----------------------MATTACFVIVGRNNSPIYETELGNAPK-\n+--------RDEAMHQHQFVLHAALDVVEDVAWTVNSMFMKGVDKFNELLV\n+STASPLMIC---PLTLLS--LPHARGSCCCT-TPAARTASKASSRKCTSS\n+TSRCRFQRLCRQILLNPLYVPGSRITSAQFDTRVRALARKYLL-------\n+--------------------------------------------------\n+-----------------\n+>3218.PP1S150_127V6.1\n+--------------------------------------------------\n+----------------------MSSTACFVIVSRNDSPIYESEVGTAPK-\n+--------KDEAAHLHQFILHASLDIVQDVVWNTNNMFLKVVDKFNDLLV\n+SVYVT-------------A--GHTRLML-LH-DSRNED---------GIK\n+NFFQEVHELYIKMLLNPLYVPGSRISSPFFDTRVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>29760.VIT_09s0002g06370.t01\n+--------------------------------------------------\n+----------------------MASTACFIIVSRNDIPIYEAEVGSAVK-\n+--------KEDAAQQHQFILHAALDVVQDLAWTTSAMFLKAIDRFNDLVV\n+SVYVT-------------A--GHILLLI-CFFQPKGAF---------NLR\n+CYVLESSL-----ISIPLSLSSCSRVSNCTAPNLGSTDRN----------\n+--------------------------------------------------\n+-----------------\n+>4641.GSMUA_Achr10P29310_001\n+--------------------------------------------------\n+----------------------MANTACFIIVSRNDIPIYEAEVGSAMK-\n+--------KEEAAQQHQFILHAALDIVEDLAWTTSAMFLKAVDKFNDLVV\n+SVYVT-------------A--GHILTTV-FR-------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------\n+>39946.BGIOSGA016720-PA\n+--------------------------------------------------\n+----------------------MASTACFAIVSKNDIPIYEAEVGSAPK-\n+--------KEDLAYQHQFILHAALDVVQDLAWSTNAMFLKSVDRFNDLVV\n+SVYVT---------------AGHIL-------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------\n+>15368.BRADI3G48660.1\n+--------------------------------------------------\n+----------------------MASTACFVIVSKNDIPIYDAEVGSAPK-\n+--------KEDQAYQHQFILHAALDVVQDLAWTTNAMSLKSVDRFNELVV\n+SVYVT---------------AGHTRFML-LH-DTRTED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>4513.MLOC_12967.5\n+--------------------------------------------------\n+----------------------MASTTCFVIVSKNDIPIYDAEVGSAPK-\n+--------KEDQAYQHQFILHAALDVVQDLAWATSAMFLKSVDRFNDLVV\n+SVYVT---------------AGHTRFML-LH-DSRSED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFNTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>4533.OB02G31210.1\n+--------------------------------------------------\n+----------------------MASTACFVIVSKNDIPIYEAEVGSAPK-\n+--------REDQAYQHQFILHAALDVVQDLAWATSTMFLKSVDRFDDLVV\n+SVYVT---------------AGHTRFML-LH-DSRSED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>39946.BGIOSGA008614-PA\n+--------------------------------------------------\n+----------------------MASTACFVIVSKNDIPIYEAEVGSAPK-\n+--------REDQAYQHQFILHAALDVVQDLAWATNTMFLKSVDRFDDLVV\n+SVYVT---------------AGHTRFML-LH-DSRSED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>39947.LOC_Os02g40000.1\n+--------------------------------------------------\n+----------------------MASTACFVIVSKNDIPIYEAEVGSAPK-\n+--------REDQAYQHQFILHAALDVVQDLAWATNTMFLKSVDRFDDLVV\n+SVYVT---------------AGHTRFML-LH-DSRSED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>4538.ORGLA02G0207300.1\n+--------------------------------------------------\n+----------------------MASTACFVIVSKNDIPIYEAEVGSAPK-\n+--------REDQAYQHQFILHAALDVVQDLAWATNTMFLKSVDRFDDLVV\n+SVYVT---------------AGHTRFML-LH-DSRSED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>39947.LOC_Os04g42500.1\n+--------------------------------------------------\n'..b'RALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>4577.GRMZM2G097568_P01\n+--MGPCWPRKARTHETQEYSRTGHSRRLFVFLPVRVGERRGVSGVRTAAV\n+DSDSVTATRRSPKLPSPQVLVGMASTACFVIVSKNDIPIYEAEVGSAPK-\n+--------KEDLSYHHQFILHAALDVVQDLAWTTNAMFLKSVDRFNDLVV\n+SVYVT---------------AGHTRFML-LH-DSRSED---------GIK\n+SFFQEVHELYIKIFLNPLYLPGSRITSSHFDTKVRALARRYL--------\n+--------------------------------------------------\n+-----------------\n+>4113.PGSC0003DMT400073367\n+MITGPTFTTA-------EFLLR----PSFTAL----------CLLCELLR\n+PVSSANSSRSLLVIELNLGIRKMASTACFMIVSRNDIPIYEAEVGTAPK-\n+--------KEDAAHQHQFILHAALDIVQDLAWTTSAMFLKSIDRFNDLVV\n+SVYVT-------------A--GHILNML----------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------\n+>4081.Solyc06g068030.2.1\n+--------------------------------------------------\n+----------------------MASTACFMIVSRNDIPIYEAEVGTAPK-\n+--------KEDAAHQHQFILHAALDIVQDLAWTTSAMFLKSIDRFNDLVV\n+SVYVT-------------AVVIHTRLML-LH-DSRNDD---------GIK\n+SFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>4113.PGSC0003DMT400073369\n+--------------------------------------------------\n+----------------------MASTACFMIVSRNDIPIYEAEVGTAPK-\n+--------KEDAAHQHQFILHAALDIVQDLAWTTSAMFLKSIDRFNDLVV\n+SVYVT-------------A--GHTRLML-LH-DSRNDD---------GIK\n+SFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>3711.Bra035176.1-P\n+--------------------------------------------------\n+----------------------MANTACFIIVGRNDIPIYEAEVGSAPK-\n+--------REDAAQLHQFILHAALDVVQDLAWTTSAMFLKSVDRFNDLVV\n+SVYVT-------------A--GHILFFS-IS-------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------\n+>3694.POPTR_0001s03500.1\n+--------------------------------------------------\n+----------------------MATTACFIIVSRDDIPIYEAEVGSATK-\n+--------REDAAQMHQFILHAALDIVQDLAWTTSAMYLKAIDRFNDLVV\n+SVYVT-------------A--GHTRLML-LH-DSRNDD---------GIK\n+SFFQEVHELYIKILLNPLYLPGSRIASSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>3847.GLYMA04G38461.1\n+--------------------------------------------------\n+----------------------MATTACFIIVSRNDIPIYEAEVGVAAK-\n+--------REDAAQLHQFILHAALDIVQDLAWTTSAMYLKSVDRFNELVV\n+SVYVT-------------A--GHTRLML-LH-DSRNDD---------GIK\n+SFFQEVHELYIKTLLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>3847.GLYMA06G16590.1\n+--------------------------------------------------\n+----------------------MATTACFIIVSRNDIPIYEAEVGVAAK-\n+--------REDSAQLHQFILHAALDIVQDLAWTTSAMYLKSVDRFNELVV\n+SVYVT-------------A--GHTRFML-LH-DSRNDD---------GIK\n+SFFQEVHELYIKTLLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>59689.Al_scaffold_0002_2746\n+--------------------------------------------------\n+----------------------MANTACFIIVGRNDIPIYEAEVGSAAKL\n+TPILSIWQREDAAQLHQFILHAALDVVQDLAWTTSAMFLKSVDRFNDLVV\n+SVYVT-------------A--GHTRLML-LH-DSRNED---------GIK\n+SFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>3702.AT1G80500.1\n+--------------------------------------------------\n+----------------------MANTACFIIVGRNDIPIYEAEVGSAAK-\n+--------REDAAQLHQFILHAALDVVQDLAWTTSAMFLKSVDRFNDLVV\n+SVYVT-------------A--GHTRLML-LH-DSRNED---------GIK\n+SFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n+>3711.Bra027566.1-P\n+--------------------------------------------------\n+----------------------MANTACFMIVARNDIPIYEAEVGSAAK-\n+--------REDAAQLHQFILHAALDVVQDLAWTTSAMFLKSVDRFNDLVV\n+SVYVTAVFKMLVCFFLNLT--THTRLML-LH-DSRNED---------GIK\n+SFFQEVHELYIKILLNPLYLPGSRITSTHFDTKVRALARKYL--------\n+--------------------------------------------------\n+-----------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.086.AA.strNOG.ENOG411BR1D.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.086.AA.strNOG.ENOG411BR1D.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,560 @@\n+>3847.GLYMA19G45090.1\n+-M----ELM--QQVK---------------------G-NYSDSREE----\n+-------------EE--A-A----AEIITIT-------------------\n+--REP--------------------------------ESSRL-HQQDAAS\n+NFGKKLDLMDLSLGS-SKEE-E-EGKLQQGGGGGG-VVHHAHEIVEKENM\n+FEKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKVW\n+RFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGLGD-LYRH-RL\n+YIDWRKRSA--HPH--AHHHA---PDPLFLP----------------SIR\n+W---------------YSLPPT-M--PPRYH---------------H---\n+DHHFHHHLNYNNLFT--------------F-QQ------HQYQLGAATAA\n+ATAAHHG-D------------------QN-SGSGSLYYLRSSMSMGGG--\n+-------------------DQN------LQGRGNNIVPMI-IDSVPVSVG\n+HH-NNRHGNGGITSGGATSSG-KRLRLFGVNMECA---S---S-AE-DS-\n+KGLSSG-SAAHVTTAAS-S--SL---HQR--LRL--------------P-\n+-L-PHEDPLSS----SSARFGDHK------GGSTGTSL--LFDLDPSLQY\n+HRQ\n+>3847.GLYMA03G42301.1\n+-M----ELM--QQVK---------------------G-NYSDSREE----\n+------E-EE---EE--A-AAITRESESS---------------------\n+----------------------------------------RL-HQQDTAS\n+NFGKKLDLMDLSLGS-SKEE-EEEGNLQQGGGG---VVHHAHQVVEKEHM\n+FEKVATPSDVGKLNRLVIPKQHAEKYFPLDSSTNEKGLLLNFEDRNGKVW\n+RFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGLGD-LYRH-RL\n+YIDWKRRPD--HAHAHPP-HH---HDPLFLP----------------SIR\n+L---------------YSLPPT-M--PPRYH---------------H---\n+DHHFHHHLNYNNLFT--------------F-QQ------HQYQQLGAATT\n+THHNNYG-Y------------------QN-SGSGSLYYLRSSMSMGGG--\n+-------------------DQN------LQGRGSNIVPMI-IDSVPVNVA\n+HHNNNRHGNGGITSGGTNCSG-KRLRLFGVNMECA-------S-SAEDS-\n+KELSSG-SAAHVTTAAS-S--SS---LHH--QRL---RV---PVPVPLED\n+PLSSSA----A----AAARFGDHK------GASTGTSL--LFDLDPSLQY\n+HRH\n+>29760.VIT_02s0025g03000.t01\n+-MIGTSSHEPNQIIRGSLRRHPPRVRKITHILLSSISLKIQLKSEIMDL-\n+--LPDRDVVCEQEQV--I-R----GKQLPFSYSSSP----SPSSSSSQYR\n+N-LVPLPNGGDR------WDAQIQ--RGWLGHQEDGMRC-FEG-------\n+GAASKLELMDTSPTN-DEDDVV-DD---------D-VRRRDSQALEREHM\n+FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSANEKGLLLNFEDRSGKPW\n+RFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGVGE-SGKD-RL\n+YIDWRRRPD--APEPS---SL---AH-HFFH----R-----------SVP\n+W------------SPLFLQA-P-V-AGGAVSMGRQQVQL-AQPNYMS-H-\n+LGGRNPYGSGAYSYN-----------------------------------\n+-----N-AV------------------NPCS--GSV------FYLRPTA-\n+--------PQQVGM--VQ---V------QQ---GGVEPMV-FNSVPV-VH\n+G----------------KAAA-KRLRLFGVNMECPIS-ESDE-------C\n+DILSSTSIPHAAVAS-Q-P--PHLSSPSSHHHPL--------QLRL----\n+-------YNGTPLPTLP----TNL------LNKGKESM--SFDLDI----\n+---\n+>4641.GSMUA_Achr5P20340_001\n+-M----YYC-TTKIS---------------------P-SFCKGDL--KMA\n+FAHGRD-MFDFTEQE--E-A----WKHAPFL-------------------\n+---------------------------------------------LSSSS\n+TSSPSSSSAPFR----WN-D-G-S--SSSS-----RR--GDDSFIEKEHM\n+FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDAEAHGKGLLLSFEDRNGESW\n+RFRYSYWSSSQSYVMTKGWSRFVKEKRLVSGDTVSFGRGVG-ESGRD-LL\n+YIDWKRRPE--NHGA---TRA----SRISFHGASFAQ-------SA--GP\n+W------------GGHLFMPRPPPPPPATVY---------------D---\n+HHRLGYGYNLQ----------------------------------P----\n+--------------------------------------------------\n+-------------------------------GGGGGSPMA-HDSVSVV-H\n+S----------------QATA-KNVRLFGVNLVCTGT-E--SK---ANGS\n+NQGASFSCL----R----S--QEA--STLPLLQF-Q--------------\n+--------HSSAESSLV----SSS------STSKEQHS--SLDLDL----\n+---\n+>4641.GSMUA_Achr9P18780_001\n+-M----EFT-SGRRDG----------------------LYIIGEE--K--\n+-------------QK--D-A----FTYPSIF-------------------\n+---------------------------------------------AL-SS\n+SSSSPSTSTAFRWHVRPC-D-G----GAA----GD-GRRESDFFTEKEHM\n+FDKVVTPSDVGKLNRLVIPKQHAE--------------------------\n+---------SQSYVMTKGWSRFVKEKRLDAGDIVSFGRGVGE-STRD-QH\n+YIDWKPRPV--NGDI---PML----PLNPLTGVSLAR-------PL--GP\n+WG-----------G------------------------------------\n+---------------------------------HTGGG-QLLFFRS-SM-\n+ARPP-Q-I-----------------------------------AAQ----\n+------------------------------RDSGSGPPMV-LSSPPLVRN\n+-----------------QAEA-KRVRLFGVNLDCPESKG-DE-----HLV\n+PSARSPSAA----Q----L--QP-A-STLPFHPL-P--------------\n+--------HGSMEFSE-----ASS------STNKDLHL--PLDLGL----\n+---\n+>4641.GSMUA_Achr5P10220_001\n+-M----EF--SIRRDG----------------------FYMTEEE--K--\n+-------------QE--E-N----SKYLSFV-------------------\n+---------------------------------------------PL-'..b'-----------------DQR----------AVVADPLV-IESVPVMMH\n+G-------GARVNQAAVGTAG-KRLRLFGVDMECGES-GGTNS-TEEE--\n+SSSSGGSLPRG---G-A-S--PS---SSM--FQL----------RL----\n+-------GNSS----ED----DHL------FKKGKSSL--PFNLDQ----\n+---\n+>3711.Bra004501.1-P\n+-M------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------MMTNLSLSR-EGEEEE-EEE-------QE-EAKKPMEEVEREHM\n+FDKVVTPSDVGKLNRLVIPKQYAERYFPLDSSTNEKGLLLNFEDLAGKSW\n+RFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRCVGD-SGRDSRL\n+FIDWRRRPK--VPDHP---TS---IA-HFAA----------------GSM\n+FP------------RFYSFP-T-A----TSY---------------N-LY\n+NYQQPRHHHH-SGYN--------------Y-PQ-----------------\n+---------------------------IP-REFGYG------YLV-----\n+-------------------DQR----------AVVADPLV-IESVPVMMH\n+G-------GAQVSQAVVGTAG-KRLRLFGVDME-------------EE--\n+SSSSGGSLPR---GD-A-S--PS---SSL--FQL----------RL----\n+-------GSSS----ED----DHF------SKKGKSSL--PFDLDQ----\n+---\n+>3711.Bra040478.1-P\n+-M------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------MTNLSLAR-EGEA----------------QVKKPIEEVEREHM\n+FDKVVTPSDVGKLNRLVIPKQHAERYFPLDSSSNEKGLLLNFEDLTGKSW\n+RFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRCVGD-S----RL\n+FIDWRRRPK--VPDYP---TS---TA-HFAA----------------GAM\n+FP------------RFYSFP-T-A-TTSTCY---------------D-LY\n+NHQPPRHHH--IGYG--------------Y-PQ-----------------\n+---------------------------IP-REFGYG------YFVRSV--\n+-------------------DQR----------AVVADPLV-IESVPVMMR\n+G-------GARVSQEVVGTAG-KRLRLFGVDME-------------EE--\n+SSSSGGSLPRAGGGG-A-S--SS---SSL--FQL----------RL----\n+-------GSSC----ED----DHF------SKKGKSSL--PFDLDQ----\n+---\n+>29760.VIT_15s0048g02370.t01\n+-M----EFG--QEM----------------------K-GFCDKEEE-QE-\n+--EEEEEEEEEEEIM--G-E----TCKVPFSSS-------SSSCASPMYK\n+G-VAPEPYRYEQQQQQRAWLGTSEPEEEAARS--YDRAALEL-GGPDGVT\n+DSSRKLEFVNLSLRN-NEDGDG-GGG-------CS-SSVGGGVCVEREHM\n+FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSASDKGLLLNFEDRDGKPW\n+RFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFERGVGE-SGKD-RL\n+YIDWRRRPD--APDPT---SL---SH-LHLPTQLPFS-------Q--SVR\n+WG------------RLYSLP-Q-S-PSMSMNMPQG-HDHMQQLNY-SSIH\n+PYHRHHHHHPHHHHHHHHHHHQRNTLGGGY-HD-----------------\n+YNA------------------------VT-SGSGSL------YYLSSS--\n+-------------------SSSHQIGAVQ---QGGDAPMV-INSVPV-VH\n+G----------------KTTA-KRLRLFGVNMECSTP-DDHP----EC--\n+NILPSTAIPH-VTMASL-S--PHLPSSSL--PPL--------QLRL----\n+-------FNGSPLQAVP----DEF------PKKGKTSL--SFDLDL----\n+---\n+>3694.POPTR_0002s18260.1\n+-M----NFV--EGE----------------------R-GDFDKEEQ-GE-\n+--EK-----QEGEEA--V-K----TSKLLFSSP-------CTSSSSTKYT\n+N-FLPEH------------------HNMWPGS--FDQSQQDS-KTQEPSL\n+NFDKKLELMELSLGN-NNETER-TSA--------D-AVVGARESIEREHM\n+FDKVVTPSDVGKLNRLVIPKQHAERYFPLDSSSNEKGLILNFEDRNGKPW\n+RFRYSYWNSSQSYVMTKGWSRFVKEKRLDAGDIVSFQRGVGE-SGKH-RL\n+FIDWRRRPN--APDPT---TF---SH-LELQNQQHYP-------Q--SVR\n+WG------------RLYSIP-Q-S-N-----LSMQ-QPQLRHLNY-S-IH\n+PYQQQQYQNRNHQNH--------------Y-HQ-----------------\n+PST------------------------IS-YGTSAQ------YYLRPP--\n+-------------------ET-LQIGAMHQQAGGSHVPLV-IDSVPV-VH\n+G----------------KTAG-KRLRLFGVNMDCPTQ-DDGQ--------\n+--SSSITMTH-GTMGSF-S--SHLASSSL-PPPL--------QLRA----\n+-------PTSAPM---Q----AEF------SKKGKNSL--SFDLDL----\n+---\n+>3694.POPTR_0014s10290.1\n+-M----NFV--GGE----------------------R-GYFDKEEQ-EE-\n+--EE-------------A-M----SSKLPFASP-------CTSSSSSKYK\n+N-FLPEH------------------QNLWPRL--FDQPRQDS-ETQEPSL\n+NFVKKLEFMELSLGN-NNESES-SST--------D-AGGGASESIEREHM\n+FDKVVTPSDVGKLNRLVIPKQHAERYFPLDSSSNEKGLLLNFEDRNGKPW\n+RFRYSYWNSSQSYVMTKGWSRFVKEKRLYAGDIVSFQRGVGE-TGKH-RL\n+FIDWRRRPN--APDPT---SF---SH-LELQNQLHYP-------Q--SLR\n+WG------------RLYSMP-Q-S-N-----LPMQ-QPQLQHLNY-S-IH\n+PYQQHQHHN--HQYH--------------Y-HQ-----------------\n+PSN------------------------IS-YGNAAQ------YYLRPP--\n+-------------------ASTLPIGAVH-EQGGSHVPVV-IDSVPV-VH\n+G----------------KTVG-KRLRLFGVNMECPTQ-NDPS--------\n+--SSVTMIRH-GTLDSL-S--PRLASSSL-PPPF--------QVRE----\n+-------PTGAPM---Q----AEF------SKKGKASL--SFDLDL----\n+---\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.087.AA.strNOG.ENOG411BRCH.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.087.AA.strNOG.ENOG411BRCH.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,195 @@
+>3711.Bra013284.1-P
+--------------------------------------MAVPLLTKKVVK
+KRSAKFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGVTLMPNVGYGSDK
+KTRHYLPNGFKKFVVHNTSDLELLMMHNRTYCAEIAHNVSTKKRKAIVER
+ASQLDIVVTNRLARLRSQEDE
+>3711.Bra021023.1-P
+--------------------------------------MAVPLLTKKVVK
+KRSAKFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGVTLMPNVGYGSDK
+KTRHYLPNGFKKFVVHNTSDLELLMMHNRTYCAEIAHNVSTKKRKAIVER
+ASQLDIVVTNRLARLRSQEDE
+>3711.Bra012616.1-P
+--------------------------------------MAVPLLTKKVVK
+KRSAKFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGVTLMPNVGYGSDK
+KTRHYLPNGFKKFVVHNTSDLELLMMHNRTYCAEIAHNVSTKKRKAIVER
+ASQLDIVVTNRLARLRSQEDE
+>3702.AT4G18100.1
+--------------------------------------MAVPLLTKKVVK
+KRSAKFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGVTLMPNVGYGSDK
+KTRHYLPNGFKKFVVHNTSELELLMMHNRTYCAEIAHNVSTKKRKAIVER
+ASQLDVVVTNRLARLRSQEDE
+>59689.fgenesh2_kg.7__2491__AT4G18100.1
+--------------------------------------MAVPLLTKKVVK
+KRSAKFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGVTLMPNVGYGSDK
+KTRHYLPNGFKKFVVHNTSELELLMMHNRTYCAEIAHNVSTKKRKSIVER
+ASQLDIVVTNRLARLRSQEDE
+>59689.fgenesh1_pg.C_scaffold_8000144
+--------------------------------------MAVPLLTKKVVK
+KRSAKFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGVTLMPNVGYGSDK
+KTRHYLPNGFKKFVVHNTSELELLMMHNRTYCAEIAHNVSTKKRKAIVER
+ASQLDIVVSNKLARLRSQEDE
+>4081.Solyc08g006900.2.1
+--------------------------------------MAVPLLTKKVVK
+KRVKQFKRPQCDRRITVKPSWRRPKGIDSRVRRKFKGCVLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNASELEILMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDVVITNKLARLRSQEDE
+>4113.PGSC0003DMT400022579
+--------------------------------------MAVPLLTKKVVK
+KRVKQFKRPQCDRRITVKPSWRRPKGIDSRVRRKFKGCVLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNASELEILMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVITNKLARLRSQEDE
+>4113.PGSC0003DMT400005838
+--------------------------------------MVVPLLNKKVVK
+KRVKRFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGCVLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNASELEILMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVITNKLARLHSQEDE
+>4081.Solyc02g070310.2.1
+--------------------------------------MAVPLLNKKVVK
+KRVKRFIRPQSDRRITVKESWRRPKGIDSRVRRKFKGCVLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNASELEILMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVITNKLARLHSQEDE
+>4513.MLOC_13746.1
+--------------------------------------MAVPILTKKIVK
+KRVKHFKRAHSDRYIGLKQSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKDIVER
+AAQLDIVVTNKLARLRSQEDE
+>4533.OB08G27830.1
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYLCLKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39947.LOC_Os08g41300.1
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYLCLKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39946.BGIOSGA029026-PA
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYLCLKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>4555.Si032237m
+-----------------------------VRKGTSSNLMAVPLLTQKIVK
+KRVKQFKRPHLDRYKCLKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>4558.Sb02g029030.1
+--------------------------------------MAVPLLTQKIVK
+KRVKQFKRPHLDRYKCLKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>4577.GRMZM2G115901_P01
+--------------------------------------MAVPLLTQKIVK
+KRVKQFKRPHLDRYKCLKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39947.LOC_Os09g32500.1
+--------------------------------------MVVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39946.BGIOSGA029496-PA
+MDSTILGFLDIRKPSLLPNSSTPPPPPPPPRRCSDRSKMAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRMYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>4538.ORGLA09G0119300.1
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39946.BGIOSGA031035-PA
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39946.BGIOSGA029494-PA
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39947.LOC_Os09g32532.1
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>39947.LOC_Os09g32520.1
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRMYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>4538.ORGLA09G0119500.1
+--------------------------------------MAVPLLTKKIVK
+KRVKQFKRPHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRMYCAEIAHNVSTKKRKEIVER
+AAQLDIVVTNKLARLRSQEDE
+>15368.BRADI4G34360.1
+--------------------------------------MAVPLLTRKIVK
+KRVKQFKRAHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKEIVER
+AAQLDVVVTNKLARLRSQEDE
+>15368.BRADI4G34340.1
+--------------------------------------MAVPLLTTKIVK
+KRVKQFKRAHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTRKRKDIVER
+AAQLDIVVTNKLARLRSQEDE
+>15368.BRADI3G40840.2
+--------------------------------------MAVPLLTTKIVK
+KRVKQFKRAHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKDIVER
+AAQLDIVVTNKLARLRSQEDE
+>15368.BRADI3G40870.1
+--------------------------------------MAVPLLTTKIVK
+KRVKQFKRAHSDRYIGLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNKFKKFVVHNVSELELLMMHNRTYCAEIAHNVSTKKRKDIVER
+AAQLDIVVTNKLARLRSQEEE
+>4641.GSMUA_Achr6P12040_001
+--------MKRTKVVPPRVHIRGSEFWDGGVDAQNAAKMAVPLLTKRIVK
+KRVKQFKRPQSDRKICVKTNWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVADLELLMMHNRTYCAEIAHNISTKKRKLIVER
+AAQLDIVVTNKLARLRSQEDE
+>4641.GSMUA_Achr7P19740_001
+--------------------------------------MAVPLLTKRIVK
+KRVKKFKRPQSDRKICVKTNWRRPKGIDSRVRRKFKGCILMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVAELELLMMHNRTYCAEIAHNISTKKRKHIVER
+AAQLDIVVTNKLARLRSQEDE
+>3847.GLYMA15G23220.1
+--------------------------------------MAVPLLSKRIVK
+KRVKKFIRPQSDRKISVKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVKDLELLMMHNRTYCAEIAHNVSTRKRKDIVER
+AAQLDVVLTNKTARLRSQEDE
+>3847.GLYMA13G06920.1
+--------------------------------------MAVPLLSKKIVK
+KRVKKFIRPQSDRKISVKPSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVKDLELLMMHNRTYCAEIAHNVSTRKRKDIVER
+AAQLDVVLTNKTARLRSQEDE
+>4641.GSMUA_Achr3P02470_001
+--------------------------------------MAVPLLTKKIVK
+KRVKKFKRPQSDRKICVKPNWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVSELDLLMMHNRTYCAEIAHNVSTRRRKSIVER
+ATQLDIVVTNKLARLRSQEDE
+>29760.VIT_10s0003g02650.t01
+--------------------------------------MAVPLLSKKIVK
+KRVKKFKRPQSDRKVSVKTNWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNAQELELLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVVTNKLARLRSQEDE
+>3694.POPTR_0002s25050.1
+--------------------------------------MAIPLLTKKIVK
+KRVKKFKRPQSDRKISVKTNWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVGELEVLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVVTNKLARLRSQEDE
+>3694.POPTR_0001s34370.1
+--------------------------------------MAVPLLTKKIVK
+KRVKKFKRPQSDRKISVKTNWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVKELEVLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVVTNKLARLRSQEDE
+>3694.POPTR_0014s18940.1
+--------------------------------------MAVPLLTKKIVK
+KRVKKFKRPQSDRKISVKTNWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNGFKKFVVHNVKELEVLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVVTNKLARLRSQEDE
+>3694.POPTR_0011s02900.1
+--------------------------------------MAVPLLTKKIVK
+KRVKKFKRPQSDRKISVKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDK
+KTRHYLPNCFKKFVVHNVKELEVLMMHNRTYCAEIAHNVSTRKRKEIVER
+AAQLDVVVTNKLARLRSQEDE

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.088.AA.strNOG.ENOG411BSXF.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.088.AA.strNOG.ENOG411BSXF.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,360 @@\n+>88036.EFJ36971\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTVKRRNGGRNKHGRGHVDPIRCSNCGRCVPKDKAVKRFLVRNIVE\n+QAAVRDVQDACVYESYTLPKLYGKMQYCVSCAIHSHVVRVRSREKRRDRN\n+PPVRPFQRRKDFVP------R-PGGPG---AA---G---GPGGPG-----\n+A---------PRPPPPR---\n+>88036.EFJ33618\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTVKRRNGGRNKHGRGHVDPIRCSNCGRCVPKDKAVKRFLVRNIVE\n+QAAVRDVQDACVYESYTLPKLYGKMQYCVSCAIHSHVVRVRSREKRRDRN\n+PPVRPFQRRKDFVP------R-PGGPG---AA---G---GPGGPG-----\n+A---------PRPPPPR---\n+>3218.PP1S169_19V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTVKRRSGGRNKHGRGHVNPIRCSNCGRCVPKDKAVKRFLVRNIVE\n+QAAVRDVQEACVYDGYVLPKLYAKMQYCISCAIHSHVVRVRSREARRIRE\n+PPQR-FR-RKEDGP-----PRVQGAPG---A--------K----------\n+-----------------A--\n+>3218.PP1S375_10V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTVKRRSGGRNKHGRGHVNPIRCSNCGRCVPKDKAVKRFLVRNIVE\n+QAAVRDVQEACVYDGYVLPKLYAKMQYCISCAIHSHVVRVRSREARRVRE\n+PPQR-FR-RKEDGP-----PRAPGAPG---A--------RPGA-------\n+-------------PGAKP--\n+>3218.PP1S270_77V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTVKRRSGGRNKHGRGHVNPIRCSNCGRCVPKDKAVKRFLVRNIVE\n+QAAVRDVQEACVYDGYVLPKLYAKMQYCISCAIHSHVVRVRSREARRIRE\n+PPQR-FR-RKEDGP-----PRAPGAPG---A--------RPGA-------\n+-------------AVAKS--\n+>4577.GRMZM5G827266_P02\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFQVRNIVE\n+QAAIRDVQEACVYDGYVLPKLYAKVHHCVSCAIHAHIVRVRSREKRRDRK\n+PPER-FR-RREDRPA------G-GQ-----GGPRPG-PGAAAT------A\n+P--------APAPVAARP--\n+>4558.Sb09g023400.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFQVRNIVE\n+QAAIRDVQEACVHDGYVLPKLYAKVHHCVSCAIHAHIVRVRSREKRRDRK\n+PPER-FR-RREDRPA------G-GQ-----GGPRPG-PGPAGA------A\n+P--------APAPVAARP--\n+>4577.GRMZM2G129015_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVHDGYVLPKLYAKVHHCVSCAIHAHIVRVRSRENRRNRE\n+PPQR-FR-RRDDGP-----R-P-GQ-----GP---P---RPGAAA-TAAP\n+P-----------AAAPRA--\n+>4555.Si037993m\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVHDGYVLPKLYAKVHHCVSCAIHAHIVRVRSRENRRNRE\n+PPQR-FR-RRDDGP-----R-P-GQ-----GA---P---RPGGGAPPAAA\n+P-----------AAAPRT--\n+>4558.Sb01g003630.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVHDGYVLPKLYAKVHHCVSCAIHAHIVRVRSRENRRNRE\n+PPQR-FR-RRDDGP-----R-P-GQ-----GP---P---RPGGAA-PAAA\n+P-----------AAAPRT--\n+>4577.GRMZM5G899149_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVHDGYVLPKLYAKVHHCVSCAIHAHIVRVRSRENRRNRE\n+PPQR-FR-RRDDGP-----R-P-GQ-----GP---P---RPGGAA-PAAA\n+A-----------AAAPRT--\n+>15368.BRADI1G04070.1\n+-------------------------------------------------'..b'---QG---P---RPAGV-GN---\n+---P----------PPRP--\n+>4641.GSMUA_Achr6P23430_001\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------MSTRQHYIFSPPCDVARLAFSQTLTRSE\n+WAATMTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACAYDGYTLPKLYIKMQYCVSCAIHSKVVRVRSRTDRRNRE\n+PPQR-FR-RRDDLPR------P----G---QG---P---RPAGA-GN---\n+---P----------P-RP--\n+>3694.POPTR_0019s08500.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHTKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQESCVYDGYVLPKLYVKMQYCVSCAIHSRVVRVRSRSERRNRE\n+PPQR-FIRRRDDMPK------P-GQPGQPGQA---P---RPAGG-A----\n+---------P----AART--\n+>3694.POPTR_0013s09160.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQESCVYDGYVLPKLYVKMQYCVSCAIHSRVVRVRSSSERRKRE\n+PPQR-FIRRRDDMPK------P-GQPGQPGQA---P---RPTGA-A----\n+---------P----A-RV--\n+>3847.GLYMA06G14950.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYEQYTLPKLYVKMQYCVSCAIHSHVVRVRSRTDRRKRE\n+PPQR-FIRRRDDAPR------P-GQPG---QA---P---RPAGV-GA---\n+---------P----A-RT--\n+>3847.GLYMA04G39940.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYEQYTLPKLYVKMQYCVSCAIHSHVVRVRSRTDRRKRE\n+PPQR-FIRRRDDAPR------P-GQPG---QA---P---RPAGV-GA---\n+---------P----A-RA--\n+>3847.GLYMA17G18200.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYEQYTLPKLYVKMQYCVSCAIHSHVVRVRSRTDRRKRD\n+PPQR-FIRRRDDAQR------P-GQPG---QA---P---RPAGT-AA---\n+---------P----V-RT--\n+>3847.GLYMA05G21370.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYEQYTLPKLYVKMQYCVSCAIHSHVVRVRSRTDRRKRE\n+PPQR-FIRRRDDAQR------P-GQPG---QA---P---RPAGT-GA---\n+---------P----V-RT--\n+>3847.GLYMA14G38950.2\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYEQYTLPKLYVKMQYCVSCAIHSHVVRVRSRTDRRKRE\n+PPQR-FIRRRDDAPR------P-GQPG---QG---P---RPAGT-AA---\n+---A-----P----V-RT--\n+>3847.GLYMA02G40660.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYEQYTLPKLYVKMQYCVSCAIHSHVVRVRSRTDRRKRE\n+PPQR-FIRRRDDAPR------P-GQPGG--QG---P---RPAGT-AA---\n+---------P----V-RT--\n+>29760.VIT_06s0004g07940.t01\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYDTYTLPKLYAKMQYCVSCAIHSHVVRVRSRTDRRKRD\n+PPLR-FR-RRDDMPK------P----G---QA---P---RPAGA-A----\n+---------A----A-RP--\n+>29760.VIT_13s0067g02700.t01\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------MGGRTGLISNPSP------AQFAAPRTR\n+SLTVMTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVE\n+QAAVRDVQEACVYDTYTLPKLYAKMQYCVSCAIHSHVVRVRSRTDRRKRD\n+PPQR-FR-RRDDMPK------P----G---QA---P---RPAGG-A----\n+---------P----V-RT--\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.089.AA.strNOG.ENOG411BV9B.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.089.AA.strNOG.ENOG411BV9B.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,300 @@\n+>4513.MLOC_22834.1\n+--------------------------------------------------\n+--------------------MAETAAIAPPPQPMAESATAAPPQPMAGNA\n+TTAAVVVVVPPP-SPPDNTMTFLCLLIAIFLPPLGVFIKYNCEVEFWICL\n+VLTFFGYFPGVIYAIWVIVKP-----------------------------\n+-------\n+>3218.PP1S203_5V6.1\n+--------------------------------------------------\n+--------------------------------------------------\n+----------MPIG-SRGAYTFVDVLLAIILPPLGVFLKYGLQSEFWICL\n+VLTILGYLPGIIYAIYVIVG------------------------------\n+-------\n+>88036.EFJ05789\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MDDSTTATCLEILLAILLPPVGVFFKYGCEIEFWICL\n+LLTVFGYIPGIIYAVYVIVGR-----------------------------\n+-------\n+>4577.GRMZM2G020666_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-ADNMVTLVRLVLAIILPPLGVFLKHGLKIEFWICL\n+LLCFFGYLPGVIYAVWVIIRKED---------------------------\n+------D\n+>4558.Sb01g034350.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MADDNTVTLVRLILAIILPPLGVFLKHGLKLEFWICL\n+ILSFFAYLPGIIYAVWVIIKKDD---------------------------\n+------D\n+>4555.Si039194m\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-ADSAVTVVRIILAIILPPLGVFLKHGIKIEFWICL\n+LLSFFAYLPGIIYAVWVIVK------------------------------\n+-------\n+>4081.Solyc01g102290.2.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MG-DSTMTCVDILLAIILPPLGVFLKFGCKVEFWICV\n+LLTLFGWLPGIVYAVWVLTK------------------------------\n+-------\n+>4113.PGSC0003DMT400046958\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MG-DSTMTCVDILLAIILPPLGVFLKFGCKVEFWICV\n+LLTLFGWLPGIVYAVWVLTK------------------------------\n+-------\n+>3711.Bra041021.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+------------M----GTATFIDILLAILLPPLGVFLRYGCGVEFWICL\n+VLTLLGYLPGILYALYVLTK------------------------------\n+-------\n+>59689.Al_scaffold_0003_571\n+--------------------------------------------------\n+--------------------------------------------------\n+------------M----GTATCVDIIIAILLPPLGVFLRFGCGVEFWICL\n+VLTLLGYIPGILYALYVLTK------------------------------\n+-------\n+>3702.AT3G05880.1\n+--------------------------------------------------\n+--------------------------------------------------\n+------------M----STATFVDIIIAILLPPLGVFLRFGCGVEFWICL\n+VLTLLGYIPGIIYAIYVLTK------------------------------\n+-------\n+>3711.Bra001171.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+------------M----GAATVVEILIAILLPPLGVFLKFGCSVEFWICL\n+ILTLLGYIPGIIYAVYAITRE-----------------------------\n+-------\n+>3711.Bra040247.1-P\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------MSTATFVEILLAILLPPLGVFLKFGLKVEFWICL\n+ILTLFGYLPGILYALYIITKD-----------------------------\n+-------\n+>59689.fgenesh1_pm.C_scaffold_3000465\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------MSTATFVEIILAIILPPLGVFLKFGCKVEFWICL\n+ILTLFGYLPGILYALYIITKRNRCFVVLFSLW------------------\n+------D\n+>3702.AT3G05890.1\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------MSTATFVEIILAIILPPLGVFLKFGCKVEFWICL\n+ILTLFGYLPGILYALYIITK------------------------------\n+-------\n+>15368.BRADI1G61460.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------MADNTATFIDLILAIILPPLGVFLKYGCEIEFWICL\n+VLSFFGYLPGIIYAVWVIVK------------------------------\n+-------\n+>39946.BGIOSGA010659-PA\n+--------------------------------------------------\n+--------------------------------------------------\n+-----M-ADRPP'..b'--------------------------\n+------------M---AGAVKCIDILIAIILPPLGVFLRFGCGVEFWICL\n+LLTILGYIPGIIYAVYAITK------------------------------\n+-------\n+>4641.GSMUA_Achr1P19010_001\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MANQGTARCIEILLAIILPPLGVFLKFGCKVEFWICL\n+LLTLFGYLPGIIYAVYAITK------------------------------\n+-------\n+>4641.GSMUA_Achr11P00650_001\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MADEGTVNCIDILVAILLPPLGVFLKFGCQVEFWICL\n+LLTLFGYLPGIIYAVYAITK------------------------------\n+-------\n+>4641.GSMUA_Achr2P18430_001\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MADEGTANCIDIILAIILPPLGVFLKFGCKAEFWICL\n+LLTILGYIPGIIYAVYAITK------------------------------\n+-------\n+>4641.GSMUA_Achr11P15890_001\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------MADEGTANCIDILLAIILPPLGVFLKFGCEMEFWICL\n+LLTLFGYIPGIIYAVYAITK------------------------------\n+-------\n+>4538.ORGLA01G0101300.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-SDGTANCIDILIAIILPPLGVFLKFGCKVEFWLCL\n+LLTFFGYLPGIIYAVYAITK------------------------------\n+-------\n+>4558.Sb03g011700.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-KEGTANCVDILIAIILPPLGVFLKFGCKVEFWLCL\n+LLTFLAYLPGIIYAIYAITKD-----------------------------\n+-------\n+>4577.GRMZM2G066870_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-KEGTANCVDILIAIILPPLGVFLKFGCKVEFWLCL\n+LLTFLAYLPGIIYAIYAITKD-----------------------------\n+-------\n+>4555.Si003690m\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-KEGTANCVDILIAIILPPLGVFLKFGCKVEFWLCL\n+LLTFLGYLPGIIYAIYAITKE-----------------------------\n+-------\n+>39946.BGIOSGA018851-PA\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M--AGTANCIDILIAIILPPLGVFLKFGCGHEFWICL\n+LLTFLGYIPGIIYAIYAITKDGLQTASSIFSIAVCLLEFGNDICIQNSVL\n+SAPILVI\n+>39947.LOC_Os05g04700.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M--AGTANCIDILIAIILPPLGVFLKFGCGHEFWICL\n+LLTFLGYIPGIIYAIYAITKDGLQTASSIFSIAVCLLEFGNDICIQNSVL\n+SAPILVI\n+>4538.ORGLA05G0024700.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M--AGTANCIDILIAIILPPLGVFLKFGCGHEFWICL\n+LLTFLGYIPGIIYAIYAITKDGLQTASSIFSIAVCLLEFGNDICIQNSVL\n+SAPILVI\n+>4513.MLOC_60357.1\n+MSP---SARHSSNVFHPFYNNASPTRATSRPSTGPHASP--RYFLPPFAS\n+PSP-PSTLDFSSPRLYNQSPAGYVCHPPPLPILLCSALLRSALLPPLH--\n+PPSEKSSPSAEG-STMAGTANCIDIILAIILPPLGVFLKFGCGHEFWICL\n+LLTFLGYIPGIIYAIYAITK------------------------------\n+-------\n+>15368.BRADI2G36770.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M--AGTANCIDIILAIILPPLGVFLKFGCGHEFWICL\n+LLTFLGYIPGIIYAIYAITK------------------------------\n+-------\n+>4558.Sb09g003060.1\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-SEGTANCVDILIAIILPPLGVFLKFGCGHQFWICL\n+LLTFLGYLPGIIYAVYAITKQ-----------------------------\n+-------\n+>4555.Si023973m\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-SERTANCVDILIAIILPPLGVFLKHGCGHEFWICL\n+LLTFLGYLPGIIYAIYAITK------------------------------\n+-------\n+>4577.GRMZM2G015605_P01\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------M-SEGTANCVDILIAIILPPLGVFLKYGCGHEFWICL\n+LLTFLGYIPGIIYAIYAITKN-----------------------------\n+------T\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.090.AA.strNOG.ENOG411BVKR.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.090.AA.strNOG.ENOG411BVKR.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,31108 @@\n+>39947.LOC_Os10g12740.1\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------MAWSQ-P-----------------------\n+--------------------------------------------------\n+--------------------VFD---------------------------\n+--------------------------------------------------\n+---------------------------PSMAAQQAS--------------\n+--------------------------------------------------\n+------------------------------P-------------------\n+--IGAGQPNT--MAQTHAQAVISPFATPYPQQGTANRV------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+----------------------------GGEKGLPLSGGIKNRPIPPQFK\n+FPPVARYSGETDPKEFLSIYESAIEAAHGDENTKAKVIHLALDGIARSWY\n+FN--LPANSIYSW------EQLRDVFVLNFQGTYEEPKTQQHLLGIRQRP\n+GQSIREYMRRFSQARCQVQDITEASVINAASA--GLLEGELTRKIAN--K\n+EPQTLEHLLRIIDAQVQVAEP-------------PPLA--------VRQ-\n+----------------------------------------PQMAIQGQPP\n+RQGQAPMTWKKFRTD----RA----------------------------G\n+KAVMAVEEVQALHKEFDAQQASNHQQP------IRKKVRK----------\n+----------------------------DLYCAFHGRSPHTIEQCRNIRQ\n+RGNVQDAR------PQQGATVEAP------------HEAVQEQTSPVEQR\n+QDAQRRVIQVITRADPPGH---LSKRQKKMQIRAVHSITSAG--EGAPQY\n+VNQLISFGPEDAEGVMF-PHQDPLVISAEIAGFEVRRIQVD--GGSSADV\n+IFAEAYAKMGLPTQALTPAPASLRGFGRE-AVQVLGQALLLIAFGSGESR\n+REEQVLFDVV---DIPYNYNAILGRATLNKFEAISHHNYL-MLKMPGPVG\n+VIVVKGLQPLAASKGDLAII-NRAVHNLEAELHSRLKHAPKP--------\n+--------------------TPHGKIV----------KVQIDDADPAKLI\n+SLGDGMGEQEAEGI------------LAVL-----KKNID-IFAWSPDEV\n+GGVLTDLIMHHLAVKPDAKPRKQKLRKMSADRQEAAKAEVQKLLRAGVIQ\n+EIDHPEWLANPVLVRKSNDKWRMCVDFTDLNKACPKDDFPLPRIDQLVDS\n+TAGCELMSFLDAYSGYHQIQMNPPDIPKIAFITPFGTFCHLRMPFGLRNA\n+GATFARLVYKVLCNQLGR-NVEAYVDDIVVKSRKAFDHASDQQETFDNLR\n+AAGIKLNPEKCVFGVRAGKLLGFLVSERGIEANPEKIDASQQMKPQSSVH\n+E'..b'-----\n+--------------------------------------------------\n+--------------------------------------------------\n+---------P--------------N-------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------PRRRARTPPPP-----PH\n+QS-------PK---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-------------------Q------------GE----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------------------------ALERVDK--------\n+---------SI--------------------ASPVAG-DA-GERRDGERR\n+LL-VYG-----------D--------GSTPQGALQAAGA------LLRH-\n+------------------------------PPVVPDPESPAQRWLDDV--\n+-ANL---------VMTA-----------QQR-------------------\n+--LGAG--------------------------------GRSAT-T-----\n+---------------------------------------KTSG-AATTGS\n+VSSRRRARRAAAVARHSAATPSST-PPTR---------------EDQHGE\n+P---DARLDI--------ERR------RNNR----------RTPR-ATE-\n+GASSSRVSPRHGR---ED-QP-SV-PPAGGVGCRAFVASLRNVRWPPRFR\n+PTITEKYDGSVNPTEFLQVYTTGIEAAGGDDRVMANFFPMVLKGQARGWL\n+MN--LPPASVHSW------EDLCQQFTMNFQGTYPRPGEEADLHAVQRGD\n+DESLRSYIQRFCQVRNTIPCIPAHAVIYAFRG--GVRHNRMLEKIAS--K\n+EPQTTAELFQLADRVARKEEA-------------WTWNPSGSGVAA----\n+-------------------------------------SAA---PGSAAQT\n+GRRDRRRKKRSVHSGDEGH-------------------------------\n+VLAVE-GAPRATRKGRPASDKKKEAGT------PSRERSA----------\n+----------------------------GKWCSVHNTSLHDLADCHAVKN\n+LAERTRKWEEDRRQERREGKSPAVPSGKRRSEAKQKAPAVDIDDGDDDLG\n+FQEPGATIATVDG-GACAH---ISRRSFKAMKRELLAAAPTHEATRRARW\n+SEVALTFDQTDHPPCVARGGQIAMVVSPTVCNVKLGRVLID--GGAALNI\n+LSPAAYDAIKAPGMVLRPSQ-PIIGVTPG-HTWPLGHIDLPVTFGGSANF\n+RTERVNFDVA---DLSLPYNAVLGRPALVKFMAAVHYAYL-QMKMSGPGG\n+PISVHGDLKVALACMEQRADHLAAAS-K----------------------\n+---------------------------PEG---GDERLGTSAPTAPRRRI\n+VTCDEVP---EDAL------------VSFL-----RANAD-VFAWRPADM\n+PGVPREVIEHRLAVRPGARPVRQKVRRQAPERQAFIREEVARLLEAGFIR\n+EVIHPEWLANPVVVPKANGKLRMCIDYTDLNKACPKDPYPLPRIDQIVDS\n+TAGCDLLCFLDAYSGYHQIRMAREDEEKTAFITPVGTYCYTSMPFGLKNA\n+GPTFQRTTRISLGSQIGRN-VEAYVDDLVVKTRNQETLLSDLAETFENLR\n+SARIKLNPDKCVFGVPAGKLLGFLVSARGIEANPEKIRAIERMRPPSKLR\n+DVQCVTGCMAALSRFISRLGEKALPLF------KLLKRSGPFTWTEEAEN\n+ALAQLKAYLSSPPVLVAPE-PNEPLLLYLAAT---PQVVSAALVVERDED\n+NPHSAHPHPVPTWPGSKQGGEAPESNGGLRPLTTGV--------------\n+--------------------------------------------------\n+GPLPACQTVLGAPDPQEGPEATAGRPHLSPFGPEANPVLTRPGREQ----\n+------------GGEAPEPNGGLRPLTTGVVPLPACPTTPGAPDPQ----\n+--------------DGPEATVGRPLLSSSDPEVIGTEDECAPRGHLDEER\n+PGDTAPSEEDRPHRRVQRPVYFVSEALRDAKTRYPQAQKMLYAILMASRK\n+LRH-YFQAHRVTVVTSYPLGQILRNREGTGRVVKWAIELSEFDLHFEPRH\n+AIKSQALADFVAEWTPTPETVSIPEASTDPSRLPHTAHWVMQFDGSLSLQ\n+GAGAGVTLTSPNGDILRYLVRLDFRATNNMAEYEGLLAGLRVAAGLGIRR\n+LLVLGDSQLVVNQVCKEYRCSDPQMDAYVRQVRRMERHFDGIELRHVPRR\n+DNMIADELSRLASSRAQTPPGAFEERLTQPSARPDPLGETDAPDRPPRP-\n+VGVQASGPEGSAPSSLRLIAWISEIQAYLTDKTLPEDREGSEHIQRISKR\n+YVLVEGTLYRRAANGILLKCIPREQGVELLADIHEGECGAHSASRTLVGK\n+AFRQGFYWPTALNDAVDLVRRCRACQFHAKQIHQPAQALQIIPLSWPFAV\n+WGLDILGPFKRAPGGFEYLYVAIDKFTKWPEAYPVVKIDKHSALKF-IKG\n+ITARFGVPNRIITDNGTQFTSELFGDYCEDMGIKLCFASPAHPRSNG--Q\n+VERANAEILKGLKTKTFNILKKHGD------------SWIEELPAVLWAN\n+RTTPSRATGETPFFLVYGAEAVLPSELTLRSPRATMYCEADQDQLRRDDL\n+DYLEERRRRAALRAARYQQ-SL-------------------RRYHQRHVR\n+ARSLCVDDLVLRRVQTRAGLSKLSPMWEGPYRVIGVPRPGSVRLATG---\n+-------------------------------------------------D\n+GTELPNPWNIEH------LR--RFY-------------P\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.codon.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.codon.fa Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,7985 @@\n+>4577.AC195313.3_FGP002\n+ATGGAGAAGAAGGCCAGCACCAAGCAGAGCAGGAAGAGGAGCGGCGACGAGGAGCAGCTG\n+ACCGAGGTGGCCGCCACCATGCCCCTGGCCAAGAAGAAGAAGCCCGACGACGAGCCCCTG\n+GCCCCCGACGCCGTGAGGGCCTGGAGGAAGAGCACCCTGAAGGAGAGCACCAACAACGAC\n+TGGAGGAACCAGTGGTTCTACATCTGCAACCACGCCCCCAACCTGCCCAAGAGGAGCGGC\n+AGGAGGCCCGAGTACAAGGACTGCTGGGTGAGCGACCTGGAGCCCGGCACCTTCAACGAG\n+ATCCCCAGCCTGCTGAAGGACATCCAGGAGCTGAAGAAGGACGGCCTGATGGGCCACAGC\n+GTGGTGCTGGACTGGCTGAAGAGGAGGTTCCAGCAGCTGCAGAGGAGGATCACCATGGGC\n+TACGAGTACCTGGGCGAGAGG\n+>4577.AC195464.4_FGP003\n+ATGGGCATGGGCATGGGCGTGAACCCCTACCCCCCCGTGTACATGGGCGACCCCGTGGGC\n+CTGTTCCTGTGCAGGGGCAGCAGGTGCACCGCCGTGGACAGCAGGAGGCCCGCCTACCTG\n+AGGATCCCCCTGCAGACCAGCATCCCCCACTACGAGGGCGAGTGGTTCTACGTGAAGAAC\n+ATCGACTGGAGCGCCCCCCCCTTCACCGACCACAAGATGGAGAGCCACGCCGAGTGGACC\n+AGGGACGTGGAGAGCAGGTACAAGAAGAAGGTGGACTACATCACCGGCAAGATCGTGGTG\n+CTGAAGGGCCAGGGCCTGAGCGGCGAGAGGCTGATCTGCACCTTCATGCAGAGGTGGCTG\n+CAGAGCCTGATGGCCAGGCAGAACCTGATGTGGAAGTACGCCGGCGAGAGCGACCCCGAC\n+AGGCACAGCAACGAGGTGCTGAGCCAGAGCGAGGTGGAGGCCAGGATCAACGACATCACC\n+GCCGGC\n+>4555.Si027349m\n+ATGGTGGGCTTCCCCAGCGCCATCAGCAGGAACGGCGCCATCAGCTTCTTCACCCTGGGC\n+GCCAGCTTCCTGGACATCGAGCCCCACTGGGACCTGTTCCACTACTTCTTCCACCTGATG\n+CCCTACCCCAACGCCGAGGCCCCCAACGTGGTGGGCGGCGCCAAGATCCAGCTGAGGGAG\n+AAGATCAGCCAGGAGTACATCCTGGTGCTGACCCTGAGCACCAACAAGGGCTGGCACGAG\n+GAGTGGTTCTACACCCCCAACCACGCCCCCACCATCCCCTGCAACATCAACGCCAGGCCC\n+AAGATGAGGGACTGCTGGACCGAGAGCATCAGGGAGGAGAACATGGGCCAGGTGTGGGAG\n+CTGGAGGCCATGATCAAGGACCTGAAGTACCACGGCCTGAACGGCATGGGCGTGGTGACC\n+AACTTCGCCTTCTGCAGGACCCAGCCCATGAAGGACTTCGTGCACCCCGCCTTCGAGTTC\n+ACCGGCGACATCGACACCAAGAGGGAGGTGCCCGAGATCGTGGACAAGGACGGCCTGTAC\n+AGGCACCTGAAGAAGTTCTTCGCCAACAACACCAGGATGAAGAACCACGGCCACATGCTG\n+CCCCTGAGCCTGTGCAACCCCAGGCCCGAGGTGAGGCTGCTGGCCTTCGTGAGCAAGGCC\n+CCCATCCCCGAGCACCCCAGGACCCTGGACATCGCCACCAGCCAGCTGAGGGAGCTGGAG\n+CTGGAGAGGCCCAAGAAGGCCAAGGCCGAGGCCGGCACCAACGGCGACAGCCCCCAGGCC\n+AGCAGCAGCCCCCAGGACAAGGCCGTGCCCAGCGGCACCAGGTGGGCCAGCACCCCCCCC\n+AAGGGCGTGGCCAGGGGCGGCTGCAGGGGCCTGGACGAGCCCCTGGTGAGGCCCAACCAC\n+CCCAGCCTGTTCCTGCCCCCCGCCAACGTGTGGCACCTGCTGCCCGAGGAGGAGAGCAGC\n+CCCCAGCACACCACCACCCCCCTGGACCTGCCCCTGGAGGAGCTGGTGCTGCACAGCATG\n+GCCAAGCTGTACCTGGGC\n+>4558.Sb10g002373.1\n+ATCGGCGCCGCCGGCATCCAGCTGAGGAGCAGGACCCCCTACGTGAGCATCCCCCAGAGG\n+ACCAGCAACAAGGGCTGGCACAGCAGGTGGTTCTACTGCAGGAACGAGAAGCCCAGCCTG\n+CCCGACTTCGTGGCCGACCACTGCCCCGTGAAGCTGCCCAGCTGGAGCAACCCCCCCAGC\n+GCCGACGAGATGGCCGAGGTGGAGAAGATCATCCCCCACCTGAACGAGCTGATCCAGGAC\n+GGCCTGAACGGCGCCGACCTGATCACCACCTTCCTGAGCAGGTGGATCCAGCCCATCAAG\n+AAGAGGTGCCACAGGATGAGCGAGTTCACCGGCAACAGCGACCCCACCAGGGAGAGCCCC\n+GTGAAGCTGCCCGAGGACGAGATCTTCAGCAGGGCCGCCCACCTGGTGAGCACCGACACC\n+AAGTTCAGGACCCACGGCAAGCCC\n+>39947.LOC_Os01g66450.1\n+ATGGCCGAGGAGAGGGAGAGCTTCGAGAGCCAGTGGGCCCCCAGCGACGTGACCGAGGAC\n+AACCTGAAGGAGATGGTGGCCCACGGCGTGCTGCCCGCCAAGGAGATCATCGGCTGGAGG\n+CCCGCCTTCGGCGAGGCCTTCCCCACCCCCGACACCCACGAGATCGTGGACACCTGGAAC\n+AGCCTGCCCATGGGCAACGAGGCCACCCAGGCCGTGGAGCTGATGGACAGGATGATCAAG\n+CTGAAGGAGCAGGGCCTGCAGGGCGAGCAGATCACCAGGCACTTCATCAAGAGCAGGCTG\n+CCCCCCATCAAGGAGAGGAGCAGGACCGCCTTCGAGTTCGACGGCAAGCACGACCCCAAC\n+AGGGAGGACCCCAAGTACCTGGACTTCAAGGTGATGAAGGAGAGGATGTACAAGATCTTC\n+AGCAACGCCATCGTGGTGAGCTACAGCCACCTGCTGCCCGTGGTGCCCTACGACGCCTTC\n+AACCCCCCCCCCCCCGAGTTCGCCCTGATGAGGAGCGACCCCCTGATCGCCCAGCACAGG\n+CTGCCCAGGGGCAAGACCAGCCAGGTGAGCGGCGGCCCCAAGATCAGGAGCGCCGACCAG\n+AGCGACACCAGCAAGCCCACCAGCCAGAGCGACTTCAGGAAGAGGAAGCTGGCCCTGAGC\n+GACGACGAGGGCGACGACGCCAAGAAGACCGGCGGCGAGGAGACCACCGGCAAGCAGCCC\n+AGGCAGGCCAACCCCAAGAAGAAGACCAGCAGCAGGCCCATGCCCAAGATCAGGAAGAGC\n+AGCAGGAGCTTCTGGAAGGACCCCAAGCCCACCGACATGGAGACCAGCAGCCTGAAGGAG\n+ACCGGCCCCACCGCCGGCGACCACAGCAGCGACAAGCAGCCCGTGACCGACAACATCGAG\n+CCCAGCAACGAGCCCCCCACCGAGAGCCAGAGCGCCGAGGCCGGCGTGGGCAGCAACCAG\n+GAGCCCCCCACCGGCAACCAGAGCGACACCGAGCAGAACAAGGACATCCCCGAGGCCGAG\n+ACCAGGGCCGACAACCCCCCCAAGAAGGACGCCAACACCGACCCCGGCAGCAGCAGCCCC\n+AGCAAGATCCAGGGCCCCACCAGGCCCAGGCCCGAGATCATCACCGGCCCCATGATCGGC\n+GACGAGGAGGAGATCCTGAGGATCAGGAGCCCCGAGGACAGCCACCCCCCCACCCTGATC\n+AAGTGGTGGGACGACGACAAGCAGCCCCAGGGCATCATCATCAACAGGCAGAAGGAGGAC\n+GAGGAGGTGTGCCTGCTGAAGAAGGCCCTGAGCCAGGCCACCCACATCGTGAACAGGATC\n+CACCTGA'..b'GGCACGCCAGCTGGTTCTACATC\n+CAGAACCTGGACCCCGCCCTGCCCGAGTACAGCTGCTGCCCCCACAAGTACCAGGACATC\n+TGGAACAGCCTGCCCATGGGCGAGGAGAGCGCCCAGGCCCTGGAGCTGCTGGACAGGCTG\n+CTGAAGCTGAAGGAGCAGGGCCTGCAGGGCGAGCAGATCACCCAGCACTTCATCAAGTGC\n+AGGCTGGCCCTGATCAAGGAGTGGAGCAGGACCGCCTTCGAGTACGACGGCAAGAACGAC\n+CCCAACAGGGAGGACCCCGACAGCATCGAGTACAAGATCATGAAGGAGAGGATGTACAAG\n+GTGTTCAGCTACGGCATCGTGCTGAGCTTCAGCCACCTGCTGCTGGTGGTGCCCTACAAC\n+GCCTTCAACCCCCCCCCCGCCGAGAACGCCCTGATGAAGAGCGACCCCCCCACCGCCCAG\n+AGGAGGAGCCCCTGGAGGCAGCAGAGCCAGGCCACCGGCGGCCCCAAGATCCAGCTGGAC\n+GCCAGGGGCAGCACCGCCGGCCCCACCGGCCAGACCGGCAGCAGGAAGAGGAAGATGATC\n+CTGAGCGACGACGACGACAGCGACCACGAGAGCGCCGGCAAGCAGCCCAAGAGGGCCGCC\n+CCCGCCAAGAAGAAGAAGACCAGCAGCGCCCAGTGCAGGAGGAGCAAGGGCCTGAGCGAG\n+ACCGCCGGCGAGGAGAAGACCGGCAGCACCGACGCCACCGAGGCCGACACCAGCAAGGAG\n+AAGCCCCCCACCGGCAGCCAGAGCGCCACCGGCGAGGCCGACGCCGACAACGAGCCCCCC\n+ACCGGCAACCAGAGCGCCAGCGCCGAGACCAGCACCAACCAGGAGCCCCTGACCGGCAAC\n+CAGCCCGGCGAGGGCACCGAGGACCCCCAGCAGCCCCACTGGGACGAGGACAAGGACATC\n+CCCGAGACCGAGGAGCACGCCAGCAGCCCCCCCCTGAACCAGAACATCGACGCCGGCCCC\n+GAGGCCAGCACCTTCGACAAGGTGGAGGGCCCCGCCTGGCCCCCCCCCAAGATCATCACC\n+GGCCCCATGATCGGCGACGAGGAGGAGATCCTGAGGATCAAGAGCACCGAGGACAGCCAG\n+GCCCCCATCCTGGTGAAGTGGTGGGACGACGAGATGCAGCCCCAGGGCATCGTGATCAAC\n+AAGAAGAAGGAGTACGAGGAGGTGGCCCTGCTGACCAAGACCCTGAACCAGGCCACCAGG\n+CTGGTGAACAGGATCCACCACAGGAACGAGGCCAAGACCGCCACCCTGGAGAGGCTGGTG\n+CCCCACCTGGACACCCTGGAGGAGACCAGGGCCAAGCTGCACGCCACCAAGGAGGAGGCC\n+AGGAGGACCGAGCACACCCTGAGGGACCAGATCGCCGAGCTGCAGGACGCCAACTTCGAG\n+TTCAGCGTGAGCAGCAAGGTGCAGGCCGCCAAGATCAGCGAGCTGGAGAGGAGGATCAAG\n+GTGCTGGAGAACGACAAGGCCGCCCTGAGCAAGGAGAGGGACCTGGCCGTGAAGGAGTTC\n+GAGGACCACAAGGGCAAGACCAAGGCCCAGTTCAACTTCCTGATCAACAAGGTGGAGGTG\n+GCCGAGAAGGCCAGGGACGAGGTGGCCAACACCACCACCCCCATCATCCAGGCCATGTAC\n+CTGAGCAGCAGCGGCACCAGCAGCCTGGACGTGGTGGAGATCTTCAACAAGCTGAGGACC\n+GCCCCCGACGTGTACTTCAAGAACATCAAGGAGGCCAGGAACATGGGCGCCAGCATGGCC\n+CTGGCCATGACCAAGAGCCTGTACCCCAAGATCGACGTGGACGCCATCGACGGCTTCGCC\n+GCCAGGACCAGCGAGGAGGACGCCCTGTACCTGATCAACGACGCC\n+>39947.LOC_Os07g11230.1\n+ATGGCCGAGGAGAGGGAGAACTTCGAGAGCCAGTGGGTGCCCAGCGACGTGATCGAGGAG\n+ACCCTGAAGGAGATGATGGCCCACGGCGTGCTGCCCGCCAAGGAGAACATCGGCTGGCAC\n+CCCGCCTTCGGCGAGGCCTTCCCCACCCCCGACACCCACGAGATCGTGGTGTTCACCCAC\n+TTCTTCTACGGCGCCAGCCAGGCCCTGGAGCTGCTGGACAGGCTGCTGAGGCTGAAGGAG\n+CAGGGCCTGCAGGAGGAGCAGATCACCCAGCACTTCATCAAGTGCAGGCTGGCCCCCATC\n+AAGGAGAGGAGCAGGACCGCCTTCGAGTACGACGGCAAGACCGACCCCAACAGGGAGGAC\n+CCCAACAGCCTGGAGTTCAAGATCATGAAGGAGAGGATGTACAAGATCTTCAGCAGCGGC\n+ATCGTGGTGAGCTTCAGCCACCTGCTGCCCATCGTGCCCTACAACGCCTTCAACCCCCCC\n+CCCGCCGCCAAGCTGCCCGGCGTGCAGAGGTTCAACCCCTGGCCCAAGAGGGACGCCATC\n+CCCCCCAGCCAGACCGTGAGCAGGAAGAGGAAGATGATCGTGAGCGACGACGACGACAGC\n+GACGACGGCCCCGTGGGCAAGCAGCCCAAGAAGGCCATCCCCCCCAAGAAGAAGACCACC\n+AGCCACCCCATGCCCAAGATCAGGAGGAGCAGCAGGAAGCCCAGCGACATCGACCCCACC\n+GGCAAGAACAGCGACCCCAGCACCAGCAGCGGCGCCGCCGAGGAGGAGAAGACCAGCAGC\n+GCCGCCGTGGCCGGCACCAACACCAGCAAGGAGAACCCCCCCACCAGCAGCCAGAGCGCC\n+ACCGGCGAGACCGAGGCCGACAACGAGCCCCCCACCGGCAACCAGAGCGCCAGCGCCGAG\n+GCCAGCACCAGCCAGGAGCCCCCCACCGGCAACCAGCCCGGCGAGGACAAGGAGAACCCC\n+CAGCAGCAGAACGTGGACGGCGAGAAGAACATCCCCGAGACCGAGGAGCAGACCAGCAGG\n+CCCCCCCTGAACCAGGACACCGACGCCGGCCCCGAGGCCAGCACCTTCGACAAGGTGGAG\n+GGCCCCGCCAGGCCCCCCCCCACCATCATCACCGGCCCCATGATCGGCGACGAGGAGGAG\n+ATCCTGAGGATCAAGAGCACCGAGGACAGCAGGCCCCCCATCCTGGTGAAGTGGTGGGAC\n+GACGAGATGCAGCCCCAGGGCATCGTGATCAACAAGCAGAAGGAGGACGGCGAGGTGGCC\n+CTGCTGACCAGGACCCTGAACCAGGCCACCAGGCTGCTGAACAGGATCCACCTGAGGAAC\n+GAGGCCAAGACCGACACCCTGGAGAAGCTGGTGCCCCACCTGGGCACCCTGGAGGAGACC\n+AGGGCCAAGCTGCACGAGACCAAGGAGGAGGCCAGGAACACCGAGCACGAGCTGAGGGAC\n+AGGATCGCCGAGCTGCAGGACGCCAACTTCGAGCTGAGCGGCAGCAGCAAGGTGCAGGCC\n+GCCAAGATCAGCGAGCTGGAGAAGAGGATCAAGGCCCTGGAGGACGAGGCCGCCCTGCCC\n+AAGGAGAAGGACCTGGCCGTGAAGGAGTTCGAGGACCACAAGGGCAAGACCAAGGCCCAG\n+TTCGACTTCCTGATCAACAAGGCCATGTACCTGAGCAACAGCGGCACCAGCAGCCTGGAC\n+ACCGTGGAGATCTTCGACAAGCTGAGGACCGCCCTGGACGTGTACTTCAAGAACATCAAG\n+GAGGCCGGCAACATGGGCGCCAGCATGGCCCTGGCCATGACCAAGAGCCTGTACCCCAAG\n+ATCAACGTGGACGCCATCGACGGCTTCGCCGCCGGCACCAGCGAGGAGGACGCCCACGAC\n+CTGATCAACGACGCCCAGAAGACCGCCGAGAGGATCGCCGTGGACGTGCTGGACAGGTTC\n+CAGAACACCAGCCTGAGCCCCGCCAACAGCGACGACGGCGAGGACGACAGCGACGAG\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.fasta Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,5434 @@\n+>4577.AC195313.3_FGP002\n+M-EKKAS--T----------------------------------------\n+-----------------KQSRKRS--GDEEQLTEVAATMPLAKKK-----\n+------KPDDE------------------------------------PLA\n+PDAV----------------------------------------------\n+-------RAW-RKS----------TL---------------KESTNNDWR\n+NQWFYICNHAPNLPKRSGR-------------------------------\n+--RPEYKDCWVSDLEPGTFNEIPSLLKDIQELKKDGLMGHSVVLDWLKRR\n+FQQLQRRITMGYEYLGER--------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------\n+>4577.AC195464.4_FGP003\n+--------------------------------------------------\n+---------------------------------MGMGMGVNP------YP\n+PVY----------------------MGDPVGLFLCRG-------------\n+-----------SRCTAVDSRRP----------------------------\n+----------------------------AYLRIPL-------QTSIPHYE\n+GEWFYVKNIDWSAPPFTDH-------------------------------\n+--KMESHAEWTRDVESRYKKKVDYITGKIVVLKGQGLSGERLICTFMQRW\n+LQSLMARQNLMWKYAGESDPDRHSNEVLS---------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------Q--SEVEARIN------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------DITAG---------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+---------------------------\n+>4555.Si027349m\n+--------------------------------------------------\n+---------------------------------------------MVGF-\n+-------PSAISR----------------------NGAISFFTLGA----\n+---------------SFLDIEPH-WDL--------FHYFFHLMPYPNAEA\n+PNVVG-GAKIQLRE----------KISQEYILVLT-------LSTNKGWH\n+EEWFYTPNHAPTIPCNINA-------------------------------\n+--RPKMRDCWTESIREENMGQVWELEAMIKDLKYHGLNGMGVVTNFAFCR\n+TQPMKDFVHPAFEFTGDIDTKREVPEIVDKDGLYRHLKKFFANNTRMKNH\n+GHMLPLS---LCNPRP-----------EVR-----LLAFVSK--APIP--\n+----------------------------------------EHPRTLDIAT\n+SQLRELELERPKKAKAE-A--G----TNGDSPQA------SS--------\n+--------------------------------------------------\n+--------------------------------------------SPQD--\n+----------------KA-----------------VPSGTRWAS------\n+--------------------------------------TPP---------\n+---------------KGVAR----------GGCRGLDEPLVRPNHPSLFL\n+PPANV---------------------------------------------\n+----WHLLPEEESSP-----------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------QHTTT--PLDLPL-----------\n+------------------------------EE--LVLHSMAKLYLG----\n+--------------------------------------------------\n+---------------------------\n+>4558.Sb10g002373.1\n+--------------------------------------------------\n+--------'..b'TKSLYPRVDID\n+AIDGFADGTSEEAALDLINDEQKAADKIAADVVERFQDFDLRPTGSDKSD\n+DEKTDTD--------------------\n+>39947.LOC_Os05g44520.1\n+M-AEERE--S----------------------------------------\n+-----------------FESQWAPSDVTEDNLKEMVAHGVLPAKEIIGWR\n+PAFGEAFPTSDTHEIVVFAHFFYGGFSLPTSRFF-RGILNFYGISLHHLN\n+PNSIVHIANFIHACEAFLGIRPH-FAL--------FRCIFFLKPQPNKSK\n+PCIVG-GAGFQLRG----------TLSQKYFSMPF-------KTSNKGWH\n+ANWFYVQNPEPVLLEYSCL-P-----------------------------\n+---PVYRDTWNSLPMGDEAAQAVELMERMIKLKEQGLQGEQITRHFIKCR\n+LAPIKERSRTAFEFDGKHDPNREDPDSLDFKVMKERMYKIFSNAIVV-SY\n+LHLLPVVPFNAFNPPPP----------EFA-----LM--KSD--PPIAQ-\n+---RRSPRH--------------QTGQGSGGPRIRSETQPSASDPIGQSD\n+SRKRKLVLSDDEADDTA-RRPGDR-ETTKKLPKQ------AT--------\n+P-R-----------------------------------------------\n+------KP--SD--IDPSGKDSDPTNVDTSSS---------KET------\n+------------EPTAEDHLSDNQPATDNVESGDQPPTGIQSAE--AEAG\n+VNQEPPTGNQS----------DAGP-SQEIPEVETQADNPR-GQDASNDR\n+RSGSPLKVSESTRPRPEIIT----------GPMIGDEEEIPRIQTAEDSC\n+PPILVKWWDDNLQPQGIVINRQKEDEEVCLLKKAL--NQATRIVN-----\n+---RIHLRNEAKTATLERLVPHLGTLEATRSQLHEARELTK-KNEHDLRD\n+RIAELQESNFELSGSSK--------------V-------NVV--------\n+---------------------QAAKISQLEKQIQTLENDKAELARQRDS-\n+------------ALKEV---------------E-------------DRKI\n+KSQAQFDVLVDKINKLEGAKDKV---ANAAT--PLIQAMFFNNAG----S\n+STLDAAEIFDKLRVATDTYFKNIKEAGSMGAS--LALAMTKSLYPRVDID\n+AIDGFVDGTSEEAALDLISDA-----------------------------\n+---------------------------\n+>39947.LOC_Os04g17720.1\n+--------------------------------------------------\n+----------------------------------------------MGY-\n+-----------THEIVVFTHFFYGDFALPTTKFF-RGILEFYGINIYHLN\n+PNSIVHIANFVHLFEAFLGIRPH-FAL--------IRRIFFLKPQPNKNK\n+PCIVG-GSSFQLRG----------TLCQKYFTLPF-------KTSNKGWH\n+ASWFYIQNLDPALPEYSCC-P-----------------------------\n+---HKYQDIWNSLPMGEESAQALELLDRLLKLKEQGLQGEQITQHFIKCR\n+LALIKEWSRTAFEYDGKNDPNREDPDSIEYKIMKERMYKVFSYGIVL-SF\n+SHLLLVVPYNAFNPPPA----------ENA-----LM--KSD--PPTAQ-\n+---RRSPWR--------------QQSQATGGPKIQLDARGSTAGPTGQTG\n+SRKRKMILSDDDDSDH---------ESAGKQPKR------AA--------\n+PAKKK-KTSSAQCR------------------------------------\n+------RS--KG--LSETAGEEK------------TGSTDATEA------\n+------------DTSKEKPPTGSQSATGEADADNEPPTGNQSAS--AETS\n+TNQEPLTGNQPGEGTEDPQQPHWDE-DKDIPETEEHASSPPLNQNIDAGP\n+EASTFDKVEGPAWPPPKIIT----------GPMIGDEEEILRIKSTEDSQ\n+APILVKWWDDEMQPQGIVINKKKEYEEVALLTKTL--NQATRLVN-----\n+---RIHHRNEAKTATLERLVPHLDTLEETRAKLHATKEEAR-RTEHTLRD\n+QIAELQDANFEFSVSSK---------------------------------\n+--------------------VQAAKISELERRIKVLENDKAALSKERDL-\n+------------AVKEF---------------E-------------DHKG\n+KTKAQFNFLINKVEVAEKARDEV---ANTTT--PIIQAMYLSSSG----T\n+SSLDVVEIFNKLRTAPDVYFKNIKEARNMGAS--MALAMTKSLYPKIDVD\n+AIDGFAARTSEEDALYLINDA-----------------------------\n+---------------------------\n+>39947.LOC_Os07g11230.1\n+M-AEERE-------------------------------------------\n+----------------NFESQWVPSDVIEETLKEMMAHGVLPAKENIGWH\n+PAFGEAFPTPDTHEIVVFTHFFYG--------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------ASQALELLDRLLRLKEQGLQEEQITQHFIKCR\n+LAPIKERSRTAFEYDGKTDPNREDPNSLEFKIMKERMYKIFSSGIVV-SF\n+SHLLPIVPYNAFNPPPA-----------------------AK--LPGVQ-\n+---RFNPWP--------------K----------------RDAIPPSQTV\n+SRKRKMIVSDDDDSDD---------GPVGKQPKK------AI--------\n+PPKKK-TTSHPMPK----IRRSS-----R---------------------\n+------KP--SD--IDPTGKNSDPSTSSGAAEEEKTSSAAVAGT------\n+------------NTSKENPPTSSQSATGETEADNEPPTGNQSAS--AEAS\n+TSQEPPTGNQPGEDKENPQQQNVDG-EKNIPETEEQTSRPPLNQDTDAGP\n+EASTFDKVEGPARPPPTIIT----------GPMIGDEEEILRIKSTEDSR\n+PPILVKWWDDEMQPQGIVINKQKEDGEVALLTRTL--NQATRLLN-----\n+---RIHLRNEAKTDTLEKLVPHLGTLEETRAKLHETKEEAR-NTEHELRD\n+RIAELQDANFELSGSSK---------------------------------\n+--------------------VQAAKISELEKRIKALE-DEAALPKEKDL-\n+------------AVKEF---------------E-------------DHKG\n+KTKAQFDFLINK-------------------------AMYLSNSG----T\n+SSLDTVEIFDKLRTALDVYFKNIKEAGNMGAS--MALAMTKSLYPKINVD\n+AIDGFAAGTSEEDAHDLINDAQKTAERIAVDVLDRFQNTSLSPANSDDGE\n+DDSDE----------------------\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.092.DNA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.092.DNA.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,104 @@
+>LcaM
+ATGGAGTCCCAAGTGCGTCAGAACTACCACCGCGACTGCGAGGCCGCCGTCAACCGTATGGTCAACATGG
+AGATGTTTGCCTCCTATACCTACACTTCAATGGCCTTTTACTTCTCCCGCGATGATGTGGCCCTTCCAGG
+CTTCTCCCATTTCTTCAAGGAGAACAGTGATGAAGAGAGGGAGCATGCTGAGAAGCTGCTGTCCTTCCAG
+AACAAGAGAGGAGGGCACATCTTCCTCCAGGACATCAAGAAACCGGAACGTGATGAGTGGGGCAGCGGGC
+TGGAGGCCATGCAGTGCGCTCTGCAGCTGAAGAAGAACGTCAACCAGGCTCTGCTGGACCTGCACAAGCT
+GGCCTCAGACCATGGAGACCCTCATCTTTGCGACTTCTTGGAGACCCACTACCTGAACGAGCAGGTGGAG
+GCCATCAAGAAGCTGGGCGACTACATCTCCAACCTCAGCCGTATGGATGCCCAGAAGAACAAGATGGCAG
+AGTACCTGTTTGACAAGCACTCTCTGGGTGGCAAGAGCTAA
+
+>LcaH
+ATGAGTTCCCAGGTGAGACAGAACTTCCACCAGGACTGCGAGGCTGCAATCAACAGGCAGATCAACCTGG
+AGCTGTACGCCTCCTACGTCTACCTGTCTATGGCGTACTACTTTGACCGGGATGACCAGGCATTGCACAA
+CTTTGCTAAGTTCTTCCGTCATCAGTCACACGAGGAGCGTGAGCACGCTGAGAAGCTCATGAAACTGCAG
+AACCAGAGGGGGGGAAGGATCTTCCTACAAGATGTCCGGAAGCCAGACAGGGACGAGTGGGGCAGCGGTG
+TTGAGGCTCTTGAATGTGCCCTGCAGCTTGAGAAGAGCGTGAACCAGTCACTGCTGGACCTGCACAAGCT
+TTGCTCTGATCACAATGACCCACATTTGTGTGATTTCATCGAGACACACTACCTGGACGAGCAGGTGAAG
+TCCATCAAAGAACTGGCAGACTGGGTGACCAACCTGCGCCGCATGGGAGCTCCTCAGAACGGCATGGCCG
+AATACCTGTTTGATAAACACACCCTGGGCAAAGAAAGCAGCTAA
+
+>Dre37936
+ATGGAGACTTCTCAGATTCGCCAGAACTACGTCCGCGACTGCGAGGCTGCGATCAACAAGATGATCAATC
+TGGAGCTTTACGCTGGATACACCTACACCTCCATGGCTCACTATTTTAAACGGGACGATGTGGCTCTTCC
+TGGATTTGCCAAGTTCTTCAAGAAGAACAGTGAGGAGGAGCGCGAACATGCTGAGAAATTCATGGAGTTC
+CAGAACAAGAGAGGTGGACGCATTGTCCTTCAGGACATCAAGAAGCCTGATCGTGATGTGTGGGGAAATG
+GGCTGATTGCTATGCAGTGTGCTCTTCAGCTGGAGAAGAACGTCAACCAGGCTCTGCTGGACCTGCATAA
+GCTCGCCACTGAGATGGGAGACCCTCATCTGTGTGATTTCCTGGAGACTCACTACCTGAATGAGCAGGTT
+GAGGCCATCAAGAAGCTTGGTGACCACATCACTAACCTCTCCAAGATGGATGCTGGAAACAACAGGATGG
+CGGAGTACCTGTTTGACAAGCACACCCTGGACAGCTAA
+
+>Tru14292
+ATGGAGTCTCAGGTGCGTCAGAACTACCACCGCGACTGCGAGGCAGCCATCAACAAAATGATCAACATGG
+AGCTGTACGCCTCTTACACCTATACTTCCATGGCCTTCTTTTTCTCCCGTGATGATGTGGCCCTTCCAGG
+CTTTGCCCATTTCTTCAAGGAGAACAGTGATGAGGAGCGGGAGCATGCTGAAAAGTTGCTCTCCTTCCAG
+AACAAGAGGGGTGGACGCATCTTCCTTCAGGACATCAAGAAACCTGAGCGTGATGAGTGGGGCAGTGGGC
+TGGAGGCCATGCAGTGTGCACTGCAGCTGGAGAAGAAGGTGAACCAAGCTCTGTTGGACCTCCACAAGCT
+CGCCTCCGACCATGTCGATCCTCATCTGTGTGATTTCCTGGAGAGCCACTACCTGAATGAGCAGGTGGAG
+GCCATCAAGAAGCTGGGTGACTACATCACCAACCTCTCCCGCATGGATGCTCAGAACAACAAGATGGCCG
+AGTACCTGTTTGACAAGCACACCCTTGGGAGCAAGAGCTAA
+
+>Ola20972
+ATGGAGTCCCAGGTGCGTCAGAACTACCACCGTGACTGTGAGGCCGCCATCAACAGGATGGTCAACATGG
+AGCTGTTTGCTTCTTACACCTACACCTCTATGGCCTTCTACTTCGACCGTGACGATGTGGCCCTTCCAGG
+TTTCTCCCATTTCTTCAAGGAGAACAGCCACGAGGAGAAGGAGCACGCGGACAAACTGCTGTCCTTCCAG
+AACAAGAGAGGAGGACGCATCTTCCTGCAGGACGTCAAGAAACCAGAGCGTGATGAGTGGGGCAGTGGGC
+TGGAAGCCATGCAGTGTGCCCTGCAGCTGGAGAAGAACGTCAACCAGGCTCTGCTGGACCTGCACAAGGT
+GGCCTCTGACCACAAAGACCCTCATATGTGTGACTTCCTGGAGACCCACTACCTGAACGAACAGGTGGAG
+TCCATCAAGAAGATTGGTGACCACATCACCAACCTCACCCGCATGGATGCTCACACCAACAAGATGGCAG
+AGTACCTGTTTGACAAGCACACCCTGGGCAGCAAAAGCTAA
+
+>Xtr21234
+ATGATTTCTCAGGTGCGTCAGAACTACAGCCATGACTGCGAGGCAGCAGTGAACCGCATGGTGAACCTGG
+AAATGTATGCTTCCTACACCTACCTGTCCATGTCCCATTATTTTGACCGTGATGATGTGGCTCTTCACCA
+CGTGGCTGAGTTCTTTAAGGAGCAGAGCAAAGAAGAGAGGGAGTGTGCCGAGAAGCTCATGAAATGCCAG
+AATAAGCGTGGGGGTCGCATTGTCCTGCAGGATATTAAGAAACCAGAGAGAGATGAGTGGGGAAGCACCC
+TGGACGCCATGCAAACAGCTTTGGATCTGGAGAAGCATGTGAACCAAGCCTTACTGGACCTGCACAACCT
+GGCAACTGAAAGAAAGGACCCACACATCTGTGACTTCCTGGAGTCGGAACACCTTGATGAGCAAGTCAAG
+CACATGAAGAAGTTTGGAGACCACATCACCAACCTGAAGCGCTTGGGGGTGCCCCAGAATGGCATGGGCG
+AGTACCTGTTCGACAAGCACAGCCTGAGCTAA
+
+>Hsa167996
+ATGACGACCGCGTCCACCTCGCAGGTGCGCCAGAACTACCACCAGGACTCAGAGGCCGCCATCAACCGCC
+AGATCAACCTGGAGCTCTACGCCTCCTACGTTTACCTGTCCATGTCTTACTACTTTGACCGCGATGATGT
+GGCTTTGAAGAACTTTGCCAAATACTTTCTTCACCAATCTCATGAGGAGAGGGAACATGCTGAGAAACTG
+ATGAAGCTGCAGAACCAACGAGGTGGCCGAATCTTCCTTCAGGATATCAAGAAACCAGACTGTGATGACT
+GGGAGAGCGGGCTGAATGCAATGGAGTGTGCATTACATTTGGAAAAAAATGTGAATCAGTCACTACTGGA
+ACTGCACAAACTGGCCACTGACAAAAATGACCCCCATTTGTGTGACTTCATTGAGACACATTACCTGAAT
+GAGCAGGTGAAAGCCATCAAAGAATTGGGTGACCACGTGACCAACTTGCGCAAGATGGGAGCGCCCGAAT
+CTGGCTTGGCGGAATATCTCTTTGACAAGCACACCCTGGGAGACAGTGATAATGAAAGCTAA
+
+>Mmu024661
+ATGACCACCGCGTCTCCCTCGCAAGTGCGCCAGAACTACCACCAGGACGCGGAGGCTGCCATCAACCGCC
+AGATCAACCTGGAGTTGTATGCCTCCTACGTCTATCTGTCTATGTCTTGTTATTTTGACCGAGATGATGT
+GGCTCTGAAGAACTTTGCCAAATACTTTCTCCACCAATCTCATGAGGAGAGGGAGCATGCCGAGAAACTG
+ATGAAGCTGCAGAACCAGCGAGGTGGCCGAATCTTCCTGCAGGATATAAAGAAACCAGACCGTGATGACT
+GGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGA
+ACTGCACAAACTGGCTACTGACAAGAATGATCCCCACTTATGTGACTTCATTGAGACGTATTATCTGAGT
+GAACAGGTGAAATCCATTAAAGAACTGGGTGACCACGTGACCAACTTACGCAAGATGGGTGCCCCTGAAG
+CTGGCATGGCAGAATATCTCTTTGACAAGCACACCCTGGGACACGGTGATGAGAGCTAA
+
+>Csa004271
+ATGTACATGGCTATGGGTCACTTCTTTGACAGAGATGATGTTGCTTTGAAAAACATCTCTGAATATTTCA
+AAGAGTGCTCAGAAGAGGAAAGAGAGCATGCAAACAAAATGATTGAGTTTCACAACAAGAGAGGCGGAAC
+TACAACTTACTTTCCAATCAAGGCACCTGGTTCATTCGATCCAGCTAATTTCAACACAATCAAGGCCATG
+AACTGTGCGCTTGCATTGGAAGTAAACGTGAACAAGAGCTTGCTTGCATTGCACGAGACTGCTAATGGTG
+ACCCGGAGTTTCAAGACTTCATAGAGGCTAACTTCTTGCATGAGCAAGTGGATGCCATCAAGAAACTCAA
+GGATTACATCACCAACCTTAAACTGGTTGGAACCGGTCTTGGCGAATTTCTGTTCGACAAGCACTTCAAG
+TCCTCCTAA
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.093.DNA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.093.DNA.fasta Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,89 @@
+>Tru14292
+ATGGAGTCTCAGGTGCGTCAGAACTACCACCGCGACTGCGAGGCAGCCATCAACAAAATGATCAACATGG
+AGCTGTACGCCTCTTACACCTATACTTCCATGGCCTTCTTTTTCTCCCGTGATGATGTGGCCCTTCCAGG
+CTTTGCCCATTTCTTCAAGGAGAACAGTGATGAGGAGCGGGAGCATGCTGAAAAGTTGCTCTCCTTCCAG
+AACAAGAGGGGTGGACGCATCTTCCTTCAGGACATCAAGAAACCTGAGCGTGATGAGTGGGGCAGTGGGC
+TGGAGGCCATGCAGTGTGCACTGCAGCTGGAGAAGAAGGTGAACCAAGCTCTGTTGGACCTCCACAAGCT
+CGCCTCCGACCATGTCGATCCTCATCTGTGTGATTTCCTGGAGAGCCACTACCTGAATGAGCAGGTGGAG
+GCCATCAAGAAGCTGGGTGACTACATCACCAACCTCTCCCGCATGGATGCTCAGAACAACAAGATGGCCG
+AGTACCTGTTTGACAAGCACACCCTTGGGAGCAAGAGC
+
+>Ola20972
+ATGGAGTCCCAGGTGCGTCAGAACTACCACCGTGACTGTGAGGCCGCCATCAACAGGATGGTCAACATGG
+AGCTGTTTGCTTCTTACACCTACACCTCTATGGCCTTCTACTTCGACCGTGACGATGTGGCCCTTCCAGG
+TTTCTCCCATTTCTTCAAGGAGAACAGCCACGAGGAGAAGGAGCACGCGGACAAACTGCTGTCCTTCCAG
+AACAAGAGAGGAGGACGCATCTTCCTGCAGGACGTCAAGAAACCAGAGCGTGATGAGTGGGGCAGTGGGC
+TGGAAGCCATGCAGTGTGCCCTGCAGCTGGAGAAGAACGTCAACCAGGCTCTGCTGGACCTGCACAAGGT
+GGCCTCTGACCACAAAGACCCTCATATGTGTGACTTCCTGGAGACCCACTACCTGAACGAACAGGTGGAG
+TCCATCAAGAAGATTGGTGACCACATCACCAACCTCACCCGCATGGATGCTCACACCAACAAGATGGCAG
+AGTACCTGTTTGACAAGCACACCCTGGGCAGCAAAAGC
+
+>LcaH
+ATGAGTTCCCAGGTGAGACAGAACTTCCACCAGGACTGCGAGGCTGCAATCAACAGGCAGATCAACCTGG
+AGCTGTACGCCTCCTACGTCTACCTGTCTATGGCGTACTACTTTGACCGGGATGACCAGGCATTGCACAA
+CTTTGCTAAGTTCTTCCGTCATCAGTCACACGAGGAGCGTGAGCACGCTGAGAAGCTCATGAAACTGCAG
+AACCAGAGGGGGGGAAGGATCTTCCTACAAGATGTCCGGAAGCCAGACAGGGACGAGTGGGGCAGCGGTG
+TTGAGGCTCTTGAATGTGCCCTGCAGCTTGAGAAGAGCGTGAACCAGTCACTGCTGGACCTGCACAAGCT
+TTGCTCTGATCACAATGACCCACATTTGTGTGATTTCATCGAGACACACTACCTGGACGAGCAGGTGAAG
+TCCATCAAAGAACTGGCAGACTGGGTGACCAACCTGCGCCGCATGGGAGCTCCTCAGAACGGCATGGCCG
+AATACCTGTTTGATAAACACACCCTGGGCAAAGAAAGCAGC
+
+>Dre37936
+ATGGAGACTTCTCAGATTCGCCAGAACTACGTCCGCGACTGCGAGGCTGCGATCAACAAGATGATCAATC
+TGGAGCTTTACGCTGGATACACCTACACCTCCATGGCTCACTATTTTAAACGGGACGATGTGGCTCTTCC
+TGGATTTGCCAAGTTCTTCAAGAAGAACAGTGAGGAGGAGCGCGAACATGCTGAGAAATTCATGGAGTTC
+CAGAACAAGAGAGGTGGACGCATTGTCCTTCAGGACATCAAGAAGCCTGATCGTGATGTGTGGGGAAATG
+GGCTGATTGCTATGCAGTGTGCTCTTCAGCTGGAGAAGAACGTCAACCAGGCTCTGCTGGACCTGCATAA
+GCTCGCCACTGAGATGGGAGACCCTCATCTGTGTGATTTCCTGGAGACTCACTACCTGAATGAGCAGGTT
+GAGGCCATCAAGAAGCTTGGTGACCACATCACTAACCTCTCCAAGATGGATGCTGGAAACAACAGGATGG
+CGGAGTACCTGTTTGACAAGCACACCCTGGACAGC
+
+>Mmu024661
+ATGACCACCGCGTCTCCCTCGCAAGTGCGCCAGAACTACCACCAGGACGCGGAGGCTGCCATCAACCGCC
+AGATCAACCTGGAGTTGTATGCCTCCTACGTCTATCTGTCTATGTCTTGTTATTTTGACCGAGATGATGT
+GGCTCTGAAGAACTTTGCCAAATACTTTCTCCACCAATCTCATGAGGAGAGGGAGCATGCCGAGAAACTG
+ATGAAGCTGCAGAACCAGCGAGGTGGCCGAATCTTCCTGCAGGATATAAAGAAACCAGACCGTGATGACT
+GGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGA
+ACTGCACAAACTGGCTACTGACAAGAATGATCCCCACTTATGTGACTTCATTGAGACGTATTATCTGAGT
+GAACAGGTGAAATCCATTAAAGAACTGGGTGACCACGTGACCAACTTACGCAAGATGGGTGCCCCTGAAG
+CTGGCATGGCAGAATATCTCTTTGACAAGCACACCCTGGGACACGGTGATGAGAGC
+
+>Xtr21234
+ATGATTTCTCAGGTGCGTCAGAACTACAGCCATGACTGCGAGGCAGCAGTGAACCGCATGGTGAACCTGG
+AAATGTATGCTTCCTACACCTACCTGTCCATGTCCCATTATTTTGACCGTGATGATGTGGCTCTTCACCA
+CGTGGCTGAGTTCTTTAAGGAGCAGAGCAAAGAAGAGAGGGAGTGTGCCGAGAAGCTCATGAAATGCCAG
+AATAAGCGTGGGGGTCGCATTGTCCTGCAGGATATTAAGAAACCAGAGAGAGATGAGTGGGGAAGCACCC
+TGGACGCCATGCAAACAGCTTTGGATCTGGAGAAGCATGTGAACCAAGCCTTACTGGACCTGCACAACCT
+GGCAACTGAAAGAAAGGACCCACACATCTGTGACTTCCTGGAGTCGGAACACCTTGATGAGCAAGTCAAG
+CACATGAAGAAGTTTGGAGACCACATCACCAACCTGAAGCGCTTGGGGGTGCCCCAGAATGGCATGGGCG
+AGTACCTGTTCGACAAGCACAGCCTGAGC
+
+>LcaM
+ATGGAGTCCCAAGTGCGTCAGAACTACCACCGCGACTGCGAGGCCGCCGTCAACCGTATGGTCAACATGG
+AGATGTTTGCCTCCTATACCTACACTTCAATGGCCTTTTACTTCTCCCGCGATGATGTGGCCCTTCCAGG
+CTTCTCCCATTTCTTCAAGGAGAACAGTGATGAAGAGAGGGAGCATGCTGAGAAGCTGCTGTCCTTCCAG
+AACAAGAGAGGAGGGCACATCTTCCTCCAGGACATCAAGAAACCGGAACGTGATGAGTGGGGCAGCGGGC
+TGGAGGCCATGCAGTGCGCTCTGCAGCTGAAGAAGAACGTCAACCAGGCTCTGCTGGACCTGCACAAGCT
+GGCCTCAGACCATGGAGACCCTCATCTTTGCGACTTCTTGGAGACCCACTACCTGAACGAGCAGGTGGAG
+GCCATCAAGAAGCTGGGCGACTACATCTCCAACCTCAGCCGTATGGATGCCCAGAAGAACAAGATGGCAG
+AGTACCTGTTTGACAAGCACTCTCTGGGTGGCAAGAGC
+
+>Csa004271
+ATGTACATGGCTATGGGTCACTTCTTTGACAGAGATGATGTTGCTTTGAAAAACATCTCTGAATATTTCA
+AAGAGTGCTCAGAAGAGGAAAGAGAGCATGCAAACAAAATGATTGAGTTTCACAACAAGAGAGGCGGAAC
+TACAACTTACTTTCCAATCAAGGCACCTGGTTCATTCGATCCAGCTAATTTCAACACAATCAAGGCCATG
+AACTGTGCGCTTGCATTGGAAGTAAACGTGAACAAGAGCTTGCTTGCATTGCACGAGACTGCTAATGGTG
+ACCCGGAGTTTCAAGACTTCATAGAGGCTAACTTCTTGCATGAGCAAGTGGATGCCATCAAGAAACTCAA
+GGATTACATCACCAACCTTAAACTGGTTGGAACCGGTCTTGGCGAATTTCTGTTCGACAAGCACTTCAAG
+TCCTCC
+
+>Hsa167996
+ATGACGACCGCGTCCACCTCGCAGGTGCGCCAGAACTACCACCAGGACTCAGAGGCCGCCATCAACCGCC
+AGATCAACCTGGAGCTCTACGCCTCCTACGTTTACCTGTCCATGTCTTACTACTTTGACCGCGATGATGT
+GGCTTTGAAGAACTTTGCCAAATACTTTCTTCACCAATCTCATGAGGAGAGGGAACATGCTGAGAAACTG
+ATGAAGCTGCAGAACCAACGAGGTGGCCGAATCTTCCTTCAGGATATCAAGAAACCAGACTGTGATGACT
+GGGAGAGCGGGCTGAATGCAATGGAGTGTGCATTACATTTGGAAAAAAATGTGAATCAGTCACTACTGGA
+ACTGCACAAACTGGCCACTGACAAAAATGACCCCCATTTGTGTGACTTCATTGAGACACATTACCTGAAT
+GAGCAGGTGAAAGCCATCAAAGAATTGGGTGACCACGTGACCAACTTGCGCAAGATGGGAGCGCCCGAAT
+CTGGCTTGGCGGAATATCTCTTTGACAAGCACACCCTGGGAGACAGTGATAATGAAAGC
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/example.094.DNADeg.sequential_phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/example.094.DNADeg.sequential_phy Fri Mar 25 17:10:43 2022 +0000

b'@@ -0,0 +1,157 @@\n+ 12 637 I\n+VRA17 CGTATAAAAT TCTAGATAGA AAACAGATAA TGACAACTTT CTATCTATTA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGCAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTAAACAGG TATAAAGGGT ACCTAGACGG GAAATCAAGC\n+ CAGAAGGGAC TAATATTCTA GAGTTTTATG GGTGAAAGTC GAATGTCTGG\n+ AGTAGAGATT AAATATTGTA ATACTGGATG GACCGACAAC GGCGTAGGCA\n+ GCTTTCTATG TAAAAACTGA CGTTGAGGGA CGAAGCCCTA GGTAGCAATA\n+ TGGATTAGAT ACCCCGGTAG TCCAGGGAGA AAATGATGAG TGCCATAGGT\n+ TAGTGAAGTT AGCCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGAGTA\n+ AGGCGGCAAC GCGCAAATTG AAATCATTAG ACCGTTCCTG AAACCAGTAA\n+ TGAAGTATGT TGTTTAATTC GATGATCCGC GAATAACCTT ACCACGTCTT\n+ GAATAC-TTT TTGTAAAAGC AGTTGTACAA GCGCTGCACG GCTGCCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAGCCCTTG\n+ ACAGTTCTCC GCTATATTGG ATAAGATAAC TGGGATT\n+VXA14085 CGTATAAAAT TCTAGATAGA AAACAGATAA TGACAACTTT CTATCTATTA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGCAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTAAACAGG TATAAAGGGT ACCTAGACGG GAAATCAAGC\n+ CAGAAGGGAC TAATATTCTA GAGTTTTATG GGTGAAAGTC GAATGTCTGG\n+ AGTAGAGATT AAATATTGTA ATACTGGATG GACCGACAAC GGCGTAGGCA\n+ GCTTTCTATG TAAAAACTGA CGTTGAGGGA CGAAGCCCTA GGTAGCAATA\n+ TGGATTAGAT ACCCCGGTAG TCCAGGGAGA AAATGATGAG TGCCATAGGT\n+ TAGTGAAGTT AGCCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGAGTA\n+ AGGCGGCAAC GCGCAAATTG AAATCATTAG ACCGTTCCTG AAACCAGTAA\n+ TGAAGTATGT TGTTTAATTC GATGATCCGC GAATAACCTT ACCACGTCTT\n+ GAATAC-TTT TTGTAAAAGC AGTTGTACAA GCGCTGCACG GCTGCCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAGCCCTTG\n+ ACAGTTCTCC GCTATATTGG ATAAGATAAC TGGGATT\n+VandXX8Z AAAATTAAAT TCTAGATAGA ATAATGATGA TGACAATTTT CTATCTATAA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGTAATACGT AGAAGACAAG\n+ TGTTATTCRT CTTTAGTGGG TTTAAAGGGT ACCTAGACAG GAAATAAAGC\n+ CAAAAGGGAC TAATTTCCTA GAGTTTTATG TGAGAATGTT GAACTATCAG\n+ AGGAGAGTCA AAATTTTTTG ATACTGGTGG GACAGGTAAC GGCGAAGGCG\n+ ACATTCTATG TAAAAACTGA CGTTGAGGAA CGAAGCCTAG GGTAGCGATA\n+ AGGATTAGAT ACCCCAGTAG TCCTAGGAGA AAATTATGAG TGCCATAGGC\n+ TAGATATATT AGTTTATAAA TGAAAGTGTA AGCATTCCAC CTCATGAGTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAACTARTAS\n+ TGAAGTATGT TATTTAATTC GATGATCCCC GAATAACCTT ACCACGCATT\n+ GCATAA---- ---------- --TATTACAA GCGCTGCACG GCTGTCTGCA\n+ GTTAATGTCG TGAGATCCTG GTTAGTTCCT TAAATTAACG AAAGCCCTTG\n+ ACGCTGGACC ATTAGCATTG GGACAATAAT AGGGACT\n+Vand17402 CGTATAAAGT TCTAGATATA ATAATGAATA TGACAATTTT ATATCTATAA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGTAATACGT AGAAGACAAG\n+ TGTTATTCAT CTTTAATGGG TTTAAAGGGT ACCTAGACAG AAAATCAAGC\n+ CAATAGGGAC TAATTTTCTA GAGTTTCAAG TGAGAATGAC GAATTACCAG\n+ AGGAGAGTCA AAATTTTATG ATACTGGTAG GACGGGTAAC GGCGAAGGCG\n+ ACATTCTATA TAAAAACTGA CGTTGAGGGA CGAAGCCTTG GGTAGCGATA\n+ AGGATTARAT ACCCTAGTAG TCCAGGGAGA AAATTATGAG TGCCATAGGC\n+ TAGATAAGTT AGCTTATAAA TGAAAGTGTA AGCATTCCAC CTCWTGAGTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAATCAGTAG\n+ TGAAGTATGT TATTTAATTC GATGGTCCGS GAATAACCTT AYCACGCTTT\n+ ---------- ---------- ---------- ---------- ----------\n+ ---------- ---------- ---------- ---------- ----------\n+ ---------- ---------- ---------- -------\n+VfunS CGTATAAAAT TCTAGATAGA AAACTGATAA TGACAACTAT CTATCTATTA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGCAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTTAAAAGG TATAAAGGGT ACCTAGACGG GGAATCAAGC\n+ CAGTAGGGAC TAATTTTCTA GAGTTTTATG GGAGAAAGTC GAATGTCTGG\n+ AGTAGAGATA TAATATTGTG ATACTAGATG GACGGGCAAC GGCGTAGGCA\n+ ACTTTCTATG TAAAAACTGA CGTTGAGGGA CGAAGCCCTG GGTAGCAATA\n+ AGGATTAGAT ACCCCAGTAG TCCAGGGAGA CAATGATGAG TGCCATAGGC\n+ T'..b'GAGGGA CGAAGCCCTG GGTAACGATA\n+ AGGATTAGAT ACCCCAGTAG TCCAGGGAGA CAATGATGAG TGCCATAGGC\n+ TAGATAAATT AGTCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGACTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAACCAGTAG\n+ TGAAGTATGT TATTTAATTC GATAATCCGC GAATAACCTT ACCACGTTTT\n+ GAATAT-CTT TTGGGGGATC ACTTTTACAA GCGCTGCACG GCTGTCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAACCCTTG\n+ ACAGTTCTCC GCTATATTGG ATAAGATAAT AGGGATT\n+Vdol16777 CGTATAAAAT TCTAGATAAA AAACTGATAA TGACAACTAT TTATCTATTA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGCAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTTATTCGG TTTAAAGGGT ACCTAGACGG GAAATCAAGC\n+ CAGTAGGGAC TAATTTTCTA GAGTTTTATG GAAGAAAGTC GAACACCTGG\n+ AGTAGAGATA AAATATTGTG ATACCAGATG GACGGGTAAC GGCGTAGGCA\n+ ACTTTCTATA TAAAAACTGA CGTTGAGGGA CGAAGCCCTG GGTAACGATA\n+ AGGATTAGAT ACCCCAGTAG TCCAGGGAGA CAATGATGAG TGCCATAGGC\n+ TAGATAAATT AGTCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGACTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAACCAGTAG\n+ TGAAGTATGT CATTTAATTC GATGATCCGC GAATAACCTT ACCACGTTTT\n+ GAATAT-CTT TTGGGGGATC GCTTATACAA GTGCTGCACG GCTGTCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAACCCTTG\n+ ACAGTTCTCC GCTATATTGG ATAAGATAAT AGGGATT\n+Vhyd16290 CGTATAAAAT TCTAGATAAA AAACTGATAA TGACAACTCT TTATCTATTA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGTAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTTATTCGG TTTAAAGGGT ACCTAGACGG KAAATCAAGC\n+ CAGTAGGGAC TAATTTTCTA GAGTTTTATG GGAGAAAGTC GAACATCTGG\n+ AGTAGAGATA AAATATTGTG ATACCAGATG GACGGGTAAC GGCGTAGGCA\n+ ACTTTCTATG TAAAAACTGA CGTTGAGGGA CGAAGCCCTG GGTAACGATA\n+ AGGATTAGAT ACCCCAGTAG TCCAGGGAGA CAATGATGAG TGCCATAGGC\n+ TAGGTAAATT AGTCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGACTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAACCAGTAG\n+ TGAAGTATGT TATTTAATTC GATAATCCGC GAATAACCTT ACCACGTTTT\n+ GAATAT-CTT TTGGGGGATC ACTTTTACAA GCGCTGCACG GCTGTCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAACCCTTG\n+ ACAGTTCTCC GCTATATTGG ATAAGATAAT AGGGATT\n+Vhyd16621 ---------- ---------- ---------- ---------- ----------\n+ -TCTTGACCA AATTACGTGC CAGCAGTCGC GGTAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTTATTCGG TTTAAAGGGT ACCTAGACGG GAAATAAAGC\n+ CAGTAGGGAC TAATTTTCTA GAGTTTTATG GGAGAAAGTC GAACATCTGG\n+ AGTAGAGATA AAATATTGTG ATACCAGATG GACGGGTAAC GGCGTAGGCA\n+ ACTTTCTATG TAAAAACTGA CGTTGAGGGA CGAAGCCCTG GGTAACGATA\n+ AGGATTAGAT ACCCCAGTAG TCCAGGGAGA CAATGATGAG TGCCATAGGC\n+ TAGGTAAATT AGTCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGACTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAACCAGTAG\n+ TGAAGTATGT TATTTAATTC GATAATCCGC GAATAACCTT ACCACGTTTT\n+ GAATAT-CTT TTGGGGGATC ACTTTTACAA GCGCTGCACG GCTGTCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAACCCTTG\n+ ---------- ---------- ---------- -------\n+Vhyd16776 CGTATAAAAT TCTAGATAAA AAACTGATRA TGACAACTCT TTATCTATTA\n+ GTCTTGACCA AATTACGTGC CAGCAGTCGC GGTAACACGC AGAAGACAAG\n+ TGTTATTCAT CTTTATTCGG TTTAAAGGGT ACCTAGACGG GAAATCAAGC\n+ CAGTAGGGAC TAATTTTCTA GAGTTTTATG GGAGAAAGTC GAACATCTGG\n+ AGTAGAGATA AAATATTGTG ATACCAGATG GACGGGTAAC GGCGTAGGCA\n+ ACTTTCTATG TAAAAACTGA CGTTGAGGGA CGAAGCCCTG GGTAACGATA\n+ AGGATTAGAT ACCCCAGTAG TCCAGGGAGA CAATGATGAG TGCCATAGGC\n+ TAGATAAATT AGTCTATAAA TGAAAGTGCA AGCATTCCAC CTCAAGACTA\n+ AAGCGGCAAC GCCCAAATTG AAATCATTAG ACCGTTTCTG AAACCAGTAG\n+ TGAAGTATGT TATTTAATTC GATAATCCGC GAATAACCTT ACCACGTTTT\n+ GAATAT-CTT TTGGGGGATC ACTTTTACAA GCGCTGCACG GCTGTCTTTA\n+ GTTAATGTCG TGAGACTTTG GTTAACTCCT TTAATTAACG AAAACCCTTG\n+ ACAGTTCTCC GCTATATTGG ATAAGATAAT AGGGATT\n\\ No newline at end of file\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/matrix.BLOSUM62
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/matrix.BLOSUM62 Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,21 @@
+a R N D C Q E G H I L k M F P S T W Y V
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0
+R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3
+N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3
+D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3
+C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
+Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2
+G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3
+H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3
+L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2
+M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1
+V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4

diff -r 000000000000 -r b15a3147e604 trimal_repo/dataset/matrix.Degenerated_DNA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/dataset/matrix.Degenerated_DNA Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,12 @@
+A C D G K M S R T W Y
+A 1 0 0 0 0 0 0 0 0 0 0
+C 0 1 0 0 0 0 0 0 0 0 0
+D 0 0 1 0 0 0 0 0 0 0 0
+G 0 0 0 1 0 0 0 0 0 0 0
+K 0 0 0 0 1 0 0 0 0 0 0
+M 0 0 0 0 0 1 0 0 0 0 0
+S 0 0 0 0 0 0 1 0 0 0 0
+R 0 0 0 0 0 0 0 1 0 0 0
+T 0 0 0 0 0 0 0 0 1 0 0
+W 0 0 0 0 0 0 0 0 0 1 0
+Y 0 0 0 0 0 0 0 0 0 0 1

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/check_codon_alignments.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/check_codon_alignments.py Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,107 @@
+#!/usr/bin/python
+
+#
+# 'check_codon_alignments.py'
+#
+# Script implemented to analyze resulting back-translated alignments by trimAl
+# Main idea here is to remove those codon-columns composed by only 'N'/'n' -
+# which are the symbol to indicate indeterminate nucleotides.
+#
+# [2014] S. Capella-Gutierrez - scapella@crg.es
+#
+# this script is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, the last available version.
+#
+# this script is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+# more details on <http://www.gnu.org/licenses/>
+#
+from Bio import AlignIO
+import numpy as np
+import argparse
+import sys
+import os
+
+def splitSequence(seq, length = 80):
+ ''' Split a given sequence contained in one line into lines of size "length"
+ '''
+ return "\n".join([seq[i:i + length] for i in range(0, len(seq), length)])
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
+ str, help = "Input alignment")
+
+ parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
+ str, help = "Set output file")
+
+ parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
+ type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
+ "phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
+
+ parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
+ type = str, help = "Set the gap symbol used in the input alignment")
+
+ parser.add_argument("--indeter_symbol", dest = "indeterSymbol", default = 'N',
+ type = str, help = "Set the indetermination symbol used in the alignment")
+
+ parser.add_argument("--keep_header", dest = "keepHeader", default = False,
+ action = "store_true", help = "Keep original alignment sequence IDs indepen"
+ + "dently of blank spaces on it")
+
+ parser.add_argument("--complementary", dest = "complement", default = False,
+ action = "store_true", help = "Get the complementary output alignment")
+
+ parser.add_argument("-v", "--verbose", dest = "verbose", default = False,
+ action = "store_true", help = "Activate verbosity")
+
+ args = parser.parse_args()
+
+ if not os.path.isfile(args.inFile):
+ sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
+
+ alignment, alignment_length = {}, 0
+ for record in AlignIO.read(args.inFile, format = args.inFormat):
+ sequence_id = record.id if not args.keepHeader else record.description
+ alignment.setdefault(sequence_id, str(record.seq))
+
+ ## Check all sequences have the same length
+ if alignment_length == 0:
+ alignment_length = len(str(record.seq))
+ if alignment_length != len(str(record.seq)):
+ sys.exit("ERROR: Check input alignment. Sequences with different lengths")
+
+ ## Check input alignment is multiple of 3
+ if (alignment_length % 3) != 0:
+ sys.exit("ERROR: Check input alignment. Its length is not multiple of 3")
+
+ indetermination_cols = []
+ indet = set([args.indeterSymbol.upper()])
+ for pos in range(0, alignment_length, 3):
+
+ onlyIndeter = True
+ for col in range(pos, pos+3):
+ column = set([alignment[seq][col].upper() for seq in alignment \
+ if alignment[seq][col] != args.gapSymbol])
+ if column ^ indet != set():
+ onlyIndeter = False
+
+ if onlyIndeter and not args.complement:
+ indetermination_cols.append(pos)
+ elif not onlyIndeter and args.complement:
+ indetermination_cols.append(pos)
+
+ if args.verbose and indetermination_cols:
+ output = ",".join(map(str, sorted(indetermination_cols)))
+ print >> sys.stderr, ("%s\t%s") % (args.inFile, output)
+
+ ofile = open(args.outFile, "w") if args.outFile else sys.stdout
+ for seq_id in alignment:
+ output = "".join([alignment[seq_id][pos:pos+3] for pos in \
+ range(0, alignment_length, 3) if not pos in indetermination_cols])
+ print >> ofile, (">%s\n%s") % (seq_id, splitSequence(output))
+ ofile.close()

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,143 @@
+#!/usr/bin/python
+import os
+import Bio
+import sys
+import random
+import argparse
+import numpy as np
+from Bio import SeqIO
+
+def splitSequence(seq, length = 80):
+ ''' Split a given sequence contained in one line into lines of size "length"
+ '''
+ return "\n".join([seq[i:i + length] for i in range(0, len(seq), length)])
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
+ str, help = "Input Codon alignment")
+
+ parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
+ str, help = "Set output file")
+
+ parser.add_argument("-s", "--numb_sequences", dest = "numb_sequences", \
+ default = 2, type = int, help = "Set how many sequences the output "
+ + "alignment should contain")
+
+ parser.add_argument("-r", "--numb_residues", dest = "numb_residues", \
+ default = 100, type = int, help = "Set how many residues the output "
+ + "alignment should contain")
+
+ parser.add_argument("-f", "--input_format", dest = "inFormat", type = str, \
+ default = "fasta", help = "Set input alignment format")
+
+ parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
+ type = str, help = "Define the gap symbol used in the input/output "
+ + "alignments")
+
+ parser.add_argument("-m", "--max_attempts", dest = "attempts", default = 10, \
+ type = int, help = "Define a maximum numnber of attempts when generating "
+ + "a random alignment before giving it up")
+
+ args = parser.parse_args()
+
+ ## Check input parameters
+ if not os.path.isfile(args.inFile):
+ sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
+
+ if args.numb_sequences < 2:
+ sys.exit(("ERROR: Check input sequences '%s'") % (str(args.numb_sequences)))
+
+ if args.numb_residues < 2:
+ sys.exit(("ERROR: Check input residues '%s'") % (str(args.numb_residues)))
+
+ if args.attempts < 1:
+ sys.exit(("ERROR: Check max. number of attempts '%s'") % (str(args.attempts)))
+
+ ## Read input alignment and get some basic information from it e.g.
+ ## sequences names, residues number, etc.
+ algLen = -1
+ alignment = {}
+ for record in SeqIO.parse(args.inFile, args.inFormat):
+ seq = str(record.seq)
+ alignment.setdefault(record.id, seq)
+ if algLen == -1:
+ algLen = len(seq)
+ if len(seq) != algLen:
+ print("Detected Inconsistencies at Sequence's length", file = sys.stderr)
+
+ sequences = list(alignment.keys())
+ columns = list(range(algLen))
+
+ ## Select randomly sequences and columns from the input alignment to populate
+ ## the output alignment controlling there are not sequences nor columns
+ ## composed only by gaps.
+
+ ## This is an iterative process
+ selected_seqs = []
+ discarded_seqs = set()
+ selected_cols = []
+ discarded_cols = set()
+
+ ## Set a counter to control how many attempts are done for generating the
+ ## random alignment
+ max_attempts = 0
+ while True:
+
+ while len(selected_seqs) < args.numb_sequences:
+ selected = random.choice(sequences)
+ if not selected in discarded_seqs:
+ selected_seqs.append(selected)
+
+ while len(selected_cols) < args.numb_residues:
+ selected = random.choice(columns)
+ if not selected in discarded_cols:
+ selected_cols.append(selected)
+
+ generated = {}
+ for seq in selected_seqs:
+ if seq in generated:
+ continue
+ ## We check generated sequences are not composed only by gaps
+ sequence = [alignment[seq][pos] for pos in selected_cols]
+ if set(sequence) - set([args.gapSymbol]) == set([]):
+ discarded_seqs.add(seq)
+ continue
+ generated.setdefault(seq, splitSequence("".join(sequence)))
+
+ ## We have to check there are not columns composed only by gaps
+ for column in range(len(selected_cols)):
+ individual_column = [generated[seq][column] for seq in generated]
+ if set(individual_column) - set([args.gapSymbol]) == set([]):
+ discarded_cols.add(selected_cols[column])
+
+ ## We check which sequences/residues remain after controlling by those
+ ## composed only by gaps
+ selected_seqs = [s for s in selected_seqs if not s in discarded_seqs]
+ selected_cols = [c for c in selected_cols if not c in discarded_cols]
+
+ if len(selected_seqs) == args.numb_sequences and \
+ len(selected_cols) == args.numb_residues:
+ break
+
+ max_attempts += 1
+ if max_attempts == args.attempts:
+ sys.exit(("ERROR: Impossible to generate random alignment after '%s' "
+ + "attempts. Check configuration") % (args.attempts))
+
+ ## Produce the output aligment.
+ n = 1
+ ofile = open(args.outFile, "w") if args.outFile else sys.stdout
+
+ ## How to properly name output sequences including a padding to have
+ ## homogeneuous ids
+ padding = int(np.ceil(np.log10(args.numb_sequences)))
+ if args.numb_sequences % 10 == 0:
+ padding += 1
+
+ for seq in selected_seqs:
+ print(">seq_%s\n%s" % (str(n).zfill(padding), generated[seq]), file = ofile)
+ n += 1
+ ofile.close()

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/get_sequence_representative_from_alignment.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/get_sequence_representative_from_alignment.py Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,95 @@
+#!/usr/bin/python
+
+#
+# 'get_sequence_representative_from_alignment.py'
+#
+# Script implemented to work with trimAl to analyze gaps statistics and decide
+# which are the boundaries in a given alignment - columns inbetween these
+# boundaries will not be removed independently of the trimming strategy
+# selected.
+#
+# [2014] S. Capella-Gutierrez - scapella@crg.es
+#
+# this script is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, the last available version.
+#
+# this script is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+# more details on <http://www.gnu.org/licenses/>
+#
+from Bio import AlignIO
+import numpy as np
+import argparse
+import sys
+import os
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
+ str, help = "Input alignment")
+
+ parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
+ str, help = "Set output file")
+
+ parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
+ type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
+ "phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
+
+ parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
+ type = str, help = "Define the gap symbol used in the input alignment")
+
+ parser.add_argument("--keep_header", dest = "keepHeader", default = False,
+ action = "store_true", help = "Keep original alignment sequence IDs indepen"
+ + "dently of blank spaces on it")
+
+ parser.add_argument("-v", "--verbose", dest = "verbose", default = False,
+ action = "store_true", help = "Activate verbosity")
+
+ args = parser.parse_args()
+
+ if not os.path.isfile(args.inFile):
+ sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
+
+ identities, sequences = {}, {}
+ for record in AlignIO.read(args.inFile, format = args.inFormat):
+ current_seq = str(record.seq)
+ sequence_length = len(current_seq)
+ sequence_id = record.id if not args.keepHeader else record.description
+
+ for seq in sequences:
+ ## Identity score is computed considering all positions for which at least
+ ## one of the sequences has a non-gap symbol
+ valid_pos = [ pos for pos in range(sequence_length) if current_seq[pos] \
+ != args.gapSymbol or sequences[seq][0][pos] == args.gapSymbol ]
+
+ identical = [ pos for pos in valid_pos if sequences[seq][0][pos] == \
+ current_seq[pos]]
+
+ ratio = float(len(identical))/len(valid_pos)
+ identities.setdefault(sequence_id, {}).setdefault(seq, ratio)
+ identities.setdefault(seq, {}).setdefault(sequence_id, ratio)
+
+ ## Save current sequence and move on to the nex one
+ ungapped = current_seq.replace(args.gapSymbol, "")
+ sequences.setdefault(sequence_id, [current_seq, ungapped, len(ungapped)])
+
+ selection, maxIdentity = set(), 0
+ for refer in sequences:
+ avg = np.average([identities[refer][seq] for seq in identities[refer]])
+ if args.verbose:
+ print >> sys.stderr, ("%-20s\t%.6f") % (refer, avg)
+ ## Save current sequence if it has a greater identity score
+ if avg > maxIdentity:
+ maxIdentity = avg
+ selection = set([(sequences[refer][1], refer)])
+ elif avg == maxIdentity:
+ selection |= set([(sequences[refer][1], refer)])
+
+ representative = sorted(selection, reverse = True)[0][1]
+ ofile = open(args.outFile, "w") if args.outFile else sys.stdout
+ print >> ofile, (">%s\n%s") % (representative, sequences[representative][1])
+ ofile.close()

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/get_sequences_gaps_ratio.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/get_sequences_gaps_ratio.py Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,78 @@
+#!/usr/bin/python3
+
+#
+# 'get_sequneces_gaps.py'
+#
+# Script implemented to obtain the sequences index for those seuqneces
+# exceding a minimum gaps' ratio threshold.
+#
+# [2020] S. Capella-Gutierrez - salvador.capella@bsc.es
+#
+# this script is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, the last available version.
+#
+# this script is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+# more details on <http://www.gnu.org/licenses/>
+#
+from Bio import AlignIO
+import argparse
+import sys
+import os
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
+ str, help = "Input alignment")
+
+ parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
+ str, help = "Set output file. It will be generated into FASTA format")
+
+ parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
+ type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
+ "phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
+
+ parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
+ type = str, help = "Define the gap symbol used in the input alignment")
+
+ parser.add_argument("--show_only_index", dest = "showIndexes", default = False, \
+ action = "store_true", help = "Show only the indexes of sequences with a "
+ + "gaps' ratio equal or higher than the established threshold")
+
+ parser.add_argument("--threshold", dest = "gapsThreshold", default = 0.0, \
+ type = float, help = "Identify sequences with a minimum of gaps' ratio")
+
+ parser.add_argument("--keep_header", dest = "keepHeader", default = False,
+ action = "store_true", help = "Keep original alignment sequence IDs indepen"
+ + "dently of blank spaces on it")
+
+ args = parser.parse_args()
+
+ if not os.path.isfile(args.inFile):
+ sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
+
+ index = 0
+ indexes = []
+ ofile = open(args.outFile, "w") if args.outFile else sys.stdout
+ for record in AlignIO.read(args.inFile, format = args.inFormat):
+ sequence_id = record.id if not args.keepHeader else record.description
+ sequence = str(record.seq)
+
+ length = len(sequence)
+ valid = len([ps for ps in range(length) if sequence[ps] != args.gapSymbol])
+ gaps_ratio = 1 - (valid/length)
+
+ if gaps_ratio >= args.gapsThreshold:
+ if not args.showIndexes:
+ print(f'{index:4d}\t{sequence_id:30}\t{gaps_ratio:.4f}', file = ofile)
+ indexes.append(index)
+ index += 1
+
+ if args.showIndexes:
+ print (','.join(map(str, indexes)), file = ofile)
+
+ ofile.close()

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/remove_shorter_sequences.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/remove_shorter_sequences.py Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,73 @@
+#!/usr/bin/python
+
+#
+# 'remove_shorter_sequences.py'
+#
+# Script implemented to explore future functionalities of trimAl. The script
+# analyzes the length of each sequence and remove those shorter than a given
+# length set by the user
+#
+# [2015] S. Capella-Gutierrez - scapella@crg.es
+#
+# this script is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, the last available version.
+#
+# this script is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+# more details on <http://www.gnu.org/licenses/>
+#
+from Bio import AlignIO
+import argparse
+import sys
+import os
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
+ str, help = "Input alignment")
+
+ parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
+ str, help = "Set output file. It will be generated into FASTA format")
+
+ parser.add_argument("-m", "--min", dest = "minLen", default = 1, type = int,
+ help = "Set a minimum sequence length to keep it in the output alignment")
+
+ parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
+ type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
+ "phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
+
+ parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
+ type = str, help = "Define the gap symbol used in the input alignment")
+
+ parser.add_argument("--keep_header", dest = "keepHeader", default = False,
+ action = "store_true", help = "Keep original alignment sequence IDs indepen"
+ + "dently of blank spaces on it")
+
+ parser.add_argument("-v", "--verbose", dest = "verbose", default = False,
+ action = "store_true", help = "Activate verbosity")
+
+ args = parser.parse_args()
+
+ if not os.path.isfile(args.inFile):
+ sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
+
+ ofile = open(args.outFile, "w") if args.outFile else sys.stdout
+ for record in AlignIO.read(args.inFile, format = args.inFormat):
+ sequence_id = record.id if not args.keepHeader else record.description
+ sequence = str(record.seq)
+
+ length = len(sequence)
+ valid = len([ps for ps in range(length) if sequence[ps] != args.gapSymbol])
+
+ if valid >= args.minLen:
+ print >> ofile, (">%s\n%s") % (sequence_id, sequence)
+ elif args.verbose:
+ msg = ("INFO: Sequence '%s' has been removed. Shorter ") % (sequence_id)
+ msg += ("(%d) than min. sequence length (%d)") % (valid, args.minLen)
+ print >> sys.stderr, msg
+ sys.stderr.flush()
+ ofile.close()

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,273 @@\n+#!/usr/bin/python\n+from Bio import SeqIO\n+from string import upper\n+import numpy as np\n+import argparse\n+import sys\n+import os\n+\n+codon_table = {\n+ ## Leucine (Leu)\n+ "TTA": "L", "TTG": "L", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L",\n+ "CTN": "L",\n+ ## Serine (Ser)\n+ "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "AGT": "S", "AGC": "S",\n+ "TCN": "S",\n+ ## Arginine (Arg)\n+ "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "AGA": "R", "AGG": "R",\n+ "CGN": "R",\n+ ## Proline (Pro)\n+ "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P",\n+ "CCN": "P",\n+ ## Glycine (Gly)\n+ "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G",\n+ "GGN": "G",\n+ ## Alanine (Ala)\n+ "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A",\n+ "GCN": "A",\n+ ## Valine (Val)\n+ "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V",\n+ "GTN": "V",\n+ ## Threonine (Thr)\n+ "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T",\n+ "ACN": "T",\n+ ## Isoleucine (Ile)\n+ "ATT": "I", "ATC": "I", "ATA": "I",\n+ ## Phenylalanine (Phe)\n+ "TTT": "F", "TTC": "F",\n+ ## Tyrosine (Tyr)\n+ "TAT": "Y", "TAC": "Y",\n+ ## Cysteine (Cys)\n+ "TGT": "C", "TGC": "C",\n+ ## Histidine (His)\n+ "CAT": "H", "CAC": "H",\n+ ## Glutamine (Gln)\n+ "CAA": "Q", "CAG": "Q",\n+ ## Aspartic acid (Asp)\n+ "GAT": "D", "GAC": "D",\n+ ## Glutamic acid (Glu)\n+ "GAA": "E", "GAG": "E",\n+ ## Lysine (Lys)\n+ "AAA": "K", "AAG": "K",\n+ ## Asparagine (Asn)\n+ "AAT": "N", "AAC": "N",\n+ ## Tryptophan (Trp)\n+ "TGG": "W", \n+ ## Methionine (M), Start\n+ "ATG": "M",\n+\n+ ## Stop codons\n+ "TGA": "U", ## Selenocysteine (Sel)\n+ "TAG": "O", ## Pyrrolysine (Pyl)\n+ "TAA": "X",\n+\n+ ## Additional characters\n+ "NNN": "X",\n+}\n+\n+stop_codons = {\n+ "TGA": "U", ## Selenocysteine (Sel)\n+ "TAG": "O", ## Pyrrolysine (Pyl)\n+ "TAA": "X",\n+}\n+\n+def _split(seq, length = 80):\n+ return "\\n".join([seq[i:i + length] for i in range(0, len(seq), length)])\n+\n+if __name__ == "__main__":\n+\n+ parser = argparse.ArgumentParser()\n+\n+ parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \\\n+ str, help = "Input Codon alignment")\n+\n+ parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \\\n+ str, help = "Set output file")\n+\n+ parser.add_argument("-l", "--log", dest = "logFile", default = None, type = \\\n+ str, help = "Set output log file")\n+\n+ parser.add_argument("-w", "--windows_size", dest = "wSize", default = 2, \\\n+ type = int, help = "Set how many columns should be analyzed before/after "\n+ + "each position")\n+\n+ parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \\\n+ type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \\\n+ "phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")\n+\n+ parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = \'-\', \\\n+ type = str, help = "Define the gap symbol used in the input alignment")\n+\n+ parser.add_argument("--discard_gaps", dest = "noGaps", action = "store_true",\n+ default = False, help = "Discard any column containing gaps prior to any "\n+ + "analysis")\n+\n+ parser.add_argument("-v", "--verbose", dest = "verbose", default = True,\n+ action = "store_false", help = "Deactivate verbosity")\n+\n+ args = parser.parse_args()\n+\n+ if not os.path.isfile(args.inFile):\n+ sys.exit(("ERROR: Check input CDS alignment file \'%s\'") % (args.inFile))\n+\n+ if args.verbose:\n+ logFile = open(args.logFile, "w") if args.logFile else sys.stderr\n+\n+ if args.wSize < 0:\n+ sys.exit(("ERROR: Check windows size \'%s\'") % (str(args.winSize)))\n+\n+ codon_table.setdefault(("%s") % (args.gapSymbol * 3), args.gapSymbol)\n+\n+ alignment_nt, alignment, incongruences = {}, {}, {}\n+ order, aligLength = [], 0\n+\n+ incongruentCodonsCols = set() \n+ for record in SeqIO.parse(args.inFile, args.inFormat):\n+ seq = str(record.seq)\n+ if record.id in alignment:\n+ sys.exit(("ERROR: Duplicated entry \'%s\'") % (record.id))\n+ if aligLength and aligLength '..b'lyses\n+ toRemove = discardedGappyCols | incongruentCodonsCols\n+ selected = sorted(set(range(initialLength)) - toRemove)\n+ aligLength = len(selected)\n+\n+ nonConservedNeighboursCols = set()\n+ \n+ ## Analyze alignment extremes: right\n+ size = args.wSize * 2\n+ upper_end = size + 1\n+ for pos in range(args.wSize):\n+ ## Check if the given column is conserved or not\n+ #~ if len(set([alignment[seq][selected[pos]] for seq in alignment])) == 1:\n+ #~ continue\n+\n+ ## Check surrounding columns to see whether all of them are conserved or not\n+ conserve = True\n+ for col in range(pos) + range(pos+1, upper_end):\n+ if len(set([alignment[seq][selected[col]] for seq in alignment])) != 1:\n+ conserve = False\n+ break\n+\n+ if not conserve:\n+ nonConservedNeighboursCols.add(selected[pos])\n+\n+ ## Analyze alignment extremes: left\n+ lower_start = aligLength - size - 1\n+ for pos in range(aligLength - args.wSize, aligLength):\n+ ## Check if the given column is conserved or not\n+ #~ if len(set([alignment[seq][selected[pos]] for seq in alignment])) == 1:\n+ #~ continue\n+\n+ ## Check surrounding columns to see whether all of them are conserved or not\n+ conserve = True\n+ for col in range(lower_start, pos) + range(pos+1, aligLength):\n+ if len(set([alignment[seq][selected[col]] for seq in alignment])) != 1:\n+ conserve = False\n+ break\n+\n+ if not conserve:\n+ nonConservedNeighboursCols.add(selected[pos])\n+\n+ ## Analyze the rest of the alignment\n+ for pos in range(args.wSize, aligLength - args.wSize):\n+\n+ ## Check whether the current column is fully conserved or not -\n+ ## In case of being fully conserved, move to next column\n+ #~ if len(set([alignment[seq][selected[pos]] for seq in alignment])) == 1:\n+ #~ continue\n+\n+ ## Check surrounding columns to see whether all of them are conserved or not\n+ conserve = True\n+ for col in range(pos - args.wSize, pos) + range(pos+1, pos+1 + args.wSize):\n+ if len(set([alignment[seq][selected[col]] for seq in alignment])) != 1:\n+ conserve = False\n+ break\n+\n+ if not conserve:\n+ nonConservedNeighboursCols.add(selected[pos])\n+ nonConservedNeighbours = len(nonConservedNeighboursCols)\n+\n+ ## Update with which columns should be removed and which ones kept\n+ toRemove |= nonConservedNeighboursCols\n+ selected = sorted(set(range(initialLength)) - toRemove)\n+\n+ ## Print some report\n+ if args.noGaps and args.verbose:\n+ if not incongruences:\n+ msg = "Initial Alignment Size:"\n+ print >> logFile, ("## Stats\\n%-58s\\t%8d") % (msg, initialLength * 3)\n+ msg = "Columns containing at least 1 gaps:"\n+ ratio = discardedGappy/float(initialLength)\n+ print >> logFile, ("%-58s\\t%8d\\t%.4f") % (msg, discardedGappy * 3, ratio)\n+ msg = "Alignment Size after trimming:"\n+ ratio = aligLength/float(initialLength)\n+ print >> logFile, ("%-58s\\t%8d\\t%.4f") % (msg, aligLength * 3, ratio)\n+ \n+ if args.verbose:\n+ if not discardedGappyCols and not incongruences:\n+ msg = "\\nInitial Alignment Size:"\n+ print >> logFile, ("## Stats\\n%-58s\\t%8d") % (msg, initialLength * 3)\n+ \n+ msg = "Columns with non-conserved neighbours:"\n+ r = nonConservedNeighbours/float(aligLength)\n+ print >> logFile,("%-58s\\t%8d\\t%.4f") % (msg, nonConservedNeighbours * 3, r)\n+ msg = "Alignment Size after trimming:"\n+ final = (aligLength-nonConservedNeighbours)\n+ ratio = final/float(initialLength)\n+ print >> logFile, ("%-58s\\t%8d\\t%.4f") % (msg, final * 3, ratio)\n+ \n+ if args.logFile:\n+ output = ",".join(map(str, sorted(toRemove)))\n+ print >> logFile, ("## Discarded Columns\\t%s") % (output)\n+\n+ ofile = open(args.outFile, "w") if args.outFile else sys.stdout\n+ if final > 0:\n+ for seqName in order:\n+ output = "".join([alignment_nt[seqName][3*pos:3*(pos+1)] for pos in selected])\n+ print >> ofile, (">%s\\n%s") % (seqName, _split(output))\n+ ofile.close()\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/scripts/set_manual_boundaries.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/set_manual_boundaries.py Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,198 @@
+#!/usr/bin/python
+
+#
+# 'set_manual_boundaries.py'
+#
+# Script implemented to work with trimAl to analyze gaps statistics and decide
+# which are the boundaries in a given alignment - columns inbetween these
+# boundaries will not be removed independently of the trimming strategy
+# selected.
+#
+# [2014] S. Capella-Gutierrez - scapella@crg.es
+#
+# this script is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, the last available version.
+#
+# this script is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+# more details on <http://www.gnu.org/licenses/>
+#
+
+import os
+import sys
+import argparse
+from string import strip
+
+def main():
+
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument("-i", "--input", dest = "inFile", required = True,
+ type = str, help = "Output file containing gaps stats generated by trimAl"
+ + " - option -sgc")
+
+ parser.add_argument("--min_gapscore_allowed", dest = "minGapBoundaries", \
+ type = float, default = .8, help = "Set the minimum gap score (1 - fraction"
+ + "of gaps) which we will use to set the boundaries when there are not "
+ + "two columns with no gaps - default 0.8")
+
+ parser.add_argument("--get_best_boundaries", dest = "bestBoundaries", default
+ = False, action = "store_true", help = "Get the best possible boundaries")
+
+ parser.add_argument("--discard_nogaps_columns", dest = "discardNoGaps",
+ default = False, action = "store_true", help = "Discard those columns with"
+ + "no gaps - otherwise, those columns will be preferentially selected as "
+ + "boundaries - this parameter will be ignored if this column are the first"
+ + "/last one to pass the input gap_score threshold")
+
+ parser.add_argument("--one_line", dest = "oneLine", default = False, action =
+ "store_true", help = "Generate output in just one line which will be used "
+ + "directly by trimAl")
+
+ args = parser.parse_args()
+
+ if not os.path.isfile(args.inFile):
+ sys.exit("ERROR: The input file should be defined")
+
+ if args.minGapBoundaries < 0 or args.minGapBoundaries > 1:
+ sys.exit("ERROR: --min_gapscore_allow should be defined in the range [0,1]")
+
+ npos = 0
+ putative = [0, 0, False, 0, 0]
+ boundaries = [-1, -1, -1, -1, -1, -1]
+ for line in open(args.inFile, "rU"):
+ ## Discard any line containing text
+ if line[0] in ["#", "|", "+"]:
+ continue
+
+ f = [chunk for chunk in map(strip, line.split("\t")) if chunk]
+ if not f:
+ continue
+ npos += 1
+ pos = int(f[0])
+ gap_score = float(f[2])
+
+ ## This function is intended to find columns - with at least one gap - which
+ ## will be used as left and right boundaries for trimAl
+ if gap_score >= args.minGapBoundaries:
+
+ ## Check whether the left boundary is defined, if that the case, define
+ ## the right one
+ if boundaries[0] != -1:
+ ## We update constantently the right boundary until the last best value
+ ## is found
+ if gap_score != 1.0:
+ boundaries[3] = pos
+ boundaries[4] = gap_score
+
+ ## Define the left boundary as the first value passing the input threshold
+ elif gap_score != 1.0:
+ boundaries[0] = pos
+ boundaries[1] = gap_score
+
+ ## Get the most to the right column without any gap
+ if gap_score == 1.0:
+ boundaries[5] = pos
+
+ ## Get the most to the left column without any gap
+ if gap_score == 1.0 and boundaries[2] == -1:
+ boundaries[2] = pos
+
+ else:
+ ## Try to get the best potential cutting points below to the input
+ ## thresholds - it would be useful if we don't found the boundaries
+
+ ## We will update the right boundary constantly
+ if gap_score > putative[4]:
+ putative[4] = gap_score
+ putative[3] = pos
+
+ ## We update current value until the left boundary is found
+ if boundaries[0] == -1:
+
+ ## Any pick on values - reflected like the at least the double of the
+ ## current best value, should be store.
+ if gap_score > (2 * putative[1]):
+ putative[1] = gap_score
+ putative[2] = False
+ putative[0] = pos
+
+ ## We update the left boundaries if and only if the immediate previous
+ ## position has at least a similar value
+ if not putative[2] and gap_score >= putative[1]:
+ putative[1] = gap_score
+ putative[0] = pos
+ else:
+ putative[2] = True
+
+ output = ""
+ ## Generate output, if any
+
+ ## First try to get the best column possible - unless the user has set-up
+ ## specifically to discard them
+ if boundaries[2] != boundaries[5] and not args.discardNoGaps:
+ if not args.oneLine:
+ ratio = float(boundaries[2])/npos
+ output = ("## %-30s\t1.0000\t") % ("NO Gaps Left Boundary")
+ output += ("pos\t%d\t%%alig\t%.4f") % (boundaries[2], ratio)
+ ratio = float(boundaries[5])/npos
+ output += ("\n## %-30s\t1.0000\t") % ("NO Gaps Right Boundary")
+ output += ("pos\t%d\t%%alig\t%.4f") % (boundaries[5], ratio)
+ else:
+ output = ("%d,%d") % (boundaries[2], boundaries[5])
+
+ elif not output and boundaries[0] != boundaries[3]:
+
+ ## If columns with no gaps are the first/last ones found - select them as
+ ## the boundaries independently of user input parameters.
+ left = boundaries[0]
+ left_score = boundaries[1]
+ if boundaries[2] != -1 and boundaries[2] < boundaries[0]:
+ left = boundaries[2]
+ left_score = 1.0
+
+ right = boundaries[3]
+ right_score = boundaries[4]
+ if boundaries[5] != -1 and boundaries[5] > boundaries[3]:
+ right = boundaries[5]
+ right_score = 1.0
+
+ if not args.oneLine:
+ ratio_l = float(left)/npos
+ ratio_r = float(right)/npos
+
+ output = ("## %-30s\t") % ("Best Gaps_Score Left Boundary")
+ output += ("%.4f\tpos\t%d\t%%alig\t%.4f\n") % (left_score, left, ratio_l)
+ output += ("## %-30s\t") % ("Best Gaps_Score Right Boundary")
+ output += ("%.4f\tpos\t%d\t%%alig\t%.4f") % (right_score, right, ratio_r)
+ else:
+ output = ("%d,%d") % (left, right)
+
+ ## If there is no output, and the user has set-up "--get_best_boundaries"
+ elif not output and args.bestBoundaries:
+ left = putatitve[0]
+ left_score = putative[1]
+
+ right = putative[3]
+ right_score = putative[4]
+
+ if not args.oneLine:
+ ratio_l = float(left)/npos
+ ratio_r = float(right)/npos
+
+ output = ("## %-30s\t") % ("Best_found Gaps_Score Left Boundary")
+ output += ("%.4f\tpos\t%d\t%%alig\t%.4f\n") % (left_score, left, ratio_l)
+ output += ("## %-30s\t") % ("Best_found Gaps_Score Right Boundary")
+ output += ("%.4f\tpos\t%d\t%%alig\t%.4f") % (right_score, right, ratio_r)
+ else:
+ output = ("%d,%d") % (left, right)
+
+ ## Generate a warning for those cases where no boundaries have been found
+ if not output:
+ output = "WARNING: OUTPUT NOT AVAILABLE"
+ print output
+### ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ****
+if __name__ == "__main__":
+ sys.exit(main())

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/alignment.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/alignment.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,3378 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ readAl v1.4: a tool for automated alignment conversion among different\n+ formats.\n+\n+ statAl v1.4: a tool for getting stats about multiple sequence alignments.\n+\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl/readAl.\n+\n+ trimAl/readAl are free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl/readAl are distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+using namespace std;\n+\n+#include <float.h>\n+#include "alignment.h"\n+#include "rwAlignment.cpp"\n+#include "autAlignment.cpp"\n+\n+#include <deque>\n+\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+/* Class constructor */\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+alignment::alignment(void) {\n+\n+ /* Alignment parameter */\n+ sequenNumber = 0;\n+ residNumber = 0;\n+\n+ /* Are the input sequences aligned? */\n+ isAligned = false;\n+\n+ /* Should the output file be reversed? */\n+ reverse = false;\n+\n+ /* Should be trimmed only terminal gaps? - set automated and manual boundaries\n+ * values */\n+ terminalGapOnly = false;\n+ left_boundary = -1;\n+ right_boundary = -1;\n+\n+ /* Input and output formats */\n+ iformat = 0;\n+ oformat = 0;\n+ shortNames = false;\n+\n+ forceCaps = false;\n+ upperCase = false;\n+ lowerCase = false;\n+\n+ /* Indicate whether sequences composed only by gaps should be kept or not */\n+ keepSequences = false;\n+\n+ /* Indicate whether original header, they may include non-alphanumerical\n+ * characters, should be dumped into output stream without any preprocessing\n+ * step */\n+ keepHeader = false;\n+\n+ gapSymbol = "-";\n+\n+ /* Sequence datatype: DNA, RNA or Protein */\n+ dataType = 0;\n+\n+ /* Window sizes to trim the input alignment */\n+ ghWindow = 0;\n+ shWindow = 0;\n+\n+ /* Minimum block size in the new alignment */\n+ blockSize = 0;\n+\n+ /* Is this alignmnet new? */\n+ oldAlignment = false;\n+\n+ /* Sequence residues number */\n+ residuesNumber = NULL;\n+\n+ /* Columns and sequences that have been previously selected */\n+ saveResidues = NULL;\n+ saveSequences = NULL;\n+\n+ /* Input sequences as well other information such as sequences name, etc */\n+ sequences = NULL;\n+ seqsName = NULL;\n+ seqsInfo = NULL;\n+\n+ /* Information about input alignment */\n+ filename = "";\n+ aligInfo = "";\n+\n+ /* Information computed from alignment */\n+ sgaps = NULL;\n+ scons = NULL;\n+ seqMatrix = NULL;\n+\n+ identities = NULL;\n+ overlaps = NULL;\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+}\n+\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+/* Class constructor */\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+alignment::alignment(string o_filename, string o_aligInfo, string *o_sequences, string *o_seqsName,\n+ string *o_seqsInfo, int o_sequenNumber, int o_residNumber, int o_iformat, int o_oformat,\n+ bool o_shortNames, int o_dataType'..b'rr << "ERROR: Sequence \\"" << seqsName[i] << "\\" has stop codon \\""\n+ << "TAG\\" (residue \\"" << aminoAcid << "\\") at position "\n+ << (int) found + 1 << " (length: " << sequences[i].length() << ")"\n+ << endl << endl;\n+ return false;\n+ }\n+ }\n+ /* Iterate over the CDS until not stop codon is found */\n+ } while(found != string::npos);\n+ }\n+\n+ /* If everything was return an OK to informat about it. */\n+ return true;\n+}\n+\n+/* Function designed to check whether input CDS file is correct or not based on\n+ * some features: Sequences are in both files (it could be more on CDS file),\n+ * they have (more or less) same ength. Otherwise, some nucleotides could be\n+ * excluded or some \'N\'s added to fit protein length. */\n+bool alignment::checkCorrespondence(string *names, int *lengths, int \\\n+ totalInputSeqs, int multiple = 1) {\n+\n+ int i, j, seqLength, indet;\n+ bool warnings = false;\n+ string tmp;\n+\n+ /* For each sequence in the current protein alignment, look for its coding\n+ * DNA sequence checking that they have the same size. */\n+ for(i = 0; i < sequenNumber; i++) {\n+\n+ /* Get protein sequence length removing any possible gap. Get as well last\n+ * residue from current sequence */\n+\n+ tmp = utils::removeCharacter(\'-\', sequences[i]);\n+ seqLength = tmp.length() * multiple;\n+ indet = ((int) tmp.length() - utils::min((int) tmp.find_last_not_of("X"), \\\n+ (int) tmp.find_last_not_of("x"))) - 1;\n+\n+ /* Go through all available CDS looking for the one with the same ID */\n+ for(j = 0; j < totalInputSeqs; j++) {\n+\n+ /* Once both ID matchs, compare its lengths */\n+ if(seqsName[i] == names[j]) {\n+\n+ /* If both sequences have the same length, stop the search */\n+ if(seqLength == lengths[j])\n+ break;\n+\n+ /* If nucleotide sequence is larger than protein sequence, warn about\n+ * it and continue the verification process. It will used the \'Nth\'\n+ * first nucleotides for the conversion */\n+ else if(seqLength < lengths[j]) {\n+ if (!warnings)\n+ cerr << endl;\n+ warnings = true;\n+ cerr << "WARNING: Sequence \\"" << seqsName[i] << "\\" will be cut at "\n+ << "position " << seqLength << " (length: "<< lengths[j] << ")"\n+ << endl;\n+ break;\n+ }\n+\n+ /* It has been detected some indeterminations at the end of the protein\n+ * sequence. That issue could be cause by some incomplete codons in the\n+ * nucleotide sequences. This issue is solved adding as much \'N\' symbols\n+ * as it is needed to preserve the backtranslated alignment */\n+ else if((indet > 0) && (indet > (seqLength - lengths[j])/3)) {\n+ if (!warnings)\n+ cerr << endl;\n+ warnings = true;\n+ cerr << "WARNING: Sequence \\"" << seqsName[i] << "\\" has some inde"\n+ << "termination symbols \'X\' at the end of sequence. They will be"\n+ << " included in the final alignment." << endl;\n+ break;\n+ }\n+\n+ /* If nucleotide sequence is shorter than protein sequence, return an\n+ * error since it is not feasible to cut the input protein aligment to\n+ * fit it into CDNA sequences size */\n+ else {\n+ if (!warnings)\n+ cerr << endl;\n+ warnings = true;\n+ cerr << "WARNING: Sequence \\"" << seqsName[i] << "\\" has less nucleo"\n+ << "tides (" << lengths[j] << ") than expected (" << seqLength\n+ << "). It will be added N\'s to complete the sequence" << endl;\n+ break;\n+ }\n+ }\n+ }\n+\n+ /* Warn about a mismatch a sequences name level */\n+ if(j == totalInputSeqs) {\n+ cerr << endl << "ERROR: Sequence \\"" << seqsName[i] << "\\" is not in "\n+ << "CDS file." << endl << endl;\n+ return false;\n+ }\n+ }\n+\n+ /* If everything is OK, return an appropiate flag */\n+ return true;\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/alignment.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/alignment.h Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,546 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ readAl v1.4: a tool for automated alignment conversion among different\n+ formats.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl/readAl.\n+\n+ trimAl/readAl are free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl/readAl are distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#ifndef ALIGNMENT_H\n+#define ALIGNMENT_H\n+\n+#include <fstream>\n+#include <iostream>\n+\n+#include <time.h>\n+\n+#include <string.h>\n+#include <stdlib.h>\n+#include <math.h>\n+\n+#include "statisticsGaps.h"\n+#include "sequencesMatrix.h"\n+#include "statisticsConservation.h"\n+#include "similarityMatrix.h"\n+#include "defines.h"\n+#include "utils.h"\n+\n+using namespace std;\n+\n+struct newValues {\n+ int residues;\n+ int sequences;\n+ string *matrix;\n+ string *seqsName;\n+};\n+\n+/** \\brief Class containing an alignment\n+ *\n+ * This class stores the alignment. It provides methods\n+ * to \\b clean the alignment and generate the clean alignment.\n+ * It also provides methods for \\b statistics \\b calculation and\n+ * \\b statistics \\b printing.\n+ */\n+\n+class alignment {\n+\n+ int sequenNumber;\n+ int residNumber;\n+\n+ bool isAligned;\n+ bool reverse;\n+\n+ bool terminalGapOnly;\n+ int left_boundary;\n+ int right_boundary;\n+\n+\n+ int iformat;\n+ int oformat;\n+ bool shortNames;\n+\n+ bool forceCaps;\n+ bool upperCase;\n+ bool lowerCase;\n+\n+ bool keepSequences;\n+ bool keepHeader;\n+\n+ string gapSymbol;\n+\n+ int dataType;\n+\n+ int ghWindow;\n+ int shWindow;\n+\n+ int blockSize;\n+\n+ string *sequences;\n+ string *seqsName;\n+ string *seqsInfo;\n+\n+ string filename;\n+ string aligInfo;\n+\n+ /* Sequences */\n+ sequencesMatrix *seqMatrix;\n+\n+ /* Statistics */\n+ statisticsGaps *sgaps;\n+ statisticsConservation *scons;\n+\n+ /* Sequences Identities */\n+ float **identities;\n+\n+ /* Sequences Overlaps */\n+ float **overlaps;\n+\n+ /* New Info */\n+ bool oldAlignment;\n+ int *residuesNumber;\n+ int *saveResidues;\n+ int *saveSequences;\n+\n+ private:\n+\n+ /* ***** Fill the matrices from the input alignment ***** */\n+ bool fillMatrices(bool aligned);\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* Alignment cleaning */\n+\n+ alignment *cleanByCutValue(double, float, const int *, bool);\n+\n+ alignment *cleanByCutValue(float, float, const float *, bool);\n+\n+ alignment *cleanByCutValue(double, const int *, float, float, const float *, bool);\n+\n+ alignment *cleanStrict(int, const int *, float, const float *, bool, bool);\n+\n+ alignment *cleanOverlapSeq(float, float *, bool);\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ public:\n+\n+ /* Constructors */\n+ alignment(void);\n+\n+ alignment(string, string, string *, string *, string *, int, int, int, int,\n+ bool, int, int, bool, bool, int, int,\n+ bool, bool, int, int, int *, int *, int *, int,\n+ int, int, float **, float **);\n+\n+ /* Overlap the operator = to use it as a constructor */\n+ alignment &'..b'matrix method.\n+ *\n+ * This method prints an alignment\'s sequence matrix.\n+ */\n+ void printSequenMatrix(void);\n+\n+ /** \\brief Returns a column from alignment\'s sequence matrix.\n+ * \\param colum, sequence matrix index\n+ * \\param columnSeqMatrix, vector used to storage a column from alignment sequence matrix.\n+ *\n+ * This method returns a column from alignment sequence matrix.\n+ */\n+ void getColumnSeqMatrix(int, int *);\n+\n+ /** \\brief Returns a column from alignment\'s sequence matrix.\n+ * \\param value to look in a sequence matrix row.\n+ * \\param sequence matrix row where look for a value.\n+ * \\param columnSeqMatrix, vector used to storage a column from alignment sequence matrix.\n+ *\n+ * Method that returns a column from the aligment\'s sequence matrix with the same value that\n+ * "value" at matrix\'s position (row, i)\n+ */\n+ void getColumnSeqMatrix(int, int, int *);\n+\n+ void setSeqMatrixOrder(int *);\n+\n+ sequencesMatrix *getSeqMatrix(void);\n+\n+ /* ********** NEW CODE ********** */\n+ /* ********** ******** ********** */\n+ int formatInputAlignment(char *);\n+\n+ int typeInputFile(void);\n+\n+ bool loadPhylipAlignment(char *);\n+\n+ bool loadFastaAlignment(char *);\n+\n+ bool loadClustalAlignment(char *);\n+\n+ bool loadNexusAlignment(char *);\n+\n+ bool loadMegaInterleavedAlignment(char *);\n+\n+ bool loadMegaNonInterleavedAlignment(char *);\n+\n+ bool loadNBRF_PirAlignment(char *);\n+\n+ bool loadPhylip3_2Alignment(char *);\n+ /* ********** ******** ********** */\n+ /* ********** ******** ********** */\n+\n+ /* Alignment to a stream */\n+ void alignmentClustalToFile(ostream &);\n+\n+ void alignmentNBRF_PirToFile(ostream &);\n+\n+ void alignmentFastaToFile(ostream &);\n+\n+ void alignmentPhylip3_2ToFile(ostream &);\n+\n+ void alignmentPhylipToFile(ostream &);\n+\n+ void alignmentPhylip_PamlToFile(ostream &);\n+\n+ void alignmentNexusToFile(ostream &);\n+\n+ void alignmentMegaToFile(ostream &);\n+\n+ bool alignmentSummaryHTML(char *, int, int, int *, int *, float *);\n+\n+ bool alignmentColourHTML(ostream &);\n+\n+ void getSequences(ostream &);\n+ /* ********** ******** ********** */\n+\n+ void saveStatistics(similarityMatrix *sm);\n+\n+ void saveStatistics(similarityMatrix *, int, int);\n+\n+ void trimTerminalGaps(bool, int *);\n+\n+ void setWindowsSize(int, int);\n+\n+ void setBlockSize(int);\n+\n+ void setOutputFormat(int, bool);\n+\n+ void setReverse(void);\n+\n+ int getInputFormat(void);\n+\n+ int getOutputFormat(void);\n+\n+ int getShortNames(void);\n+\n+ int getReverse(void);\n+\n+ int getBlockSize(void);\n+\n+ void calculateSeqIdentity(void);\n+\n+ // New\n+ void calculateRelaxedSeqIdentity(void);\n+\n+ // New\n+ void calculateSeqOverlap(void);\n+\n+ void printSeqOverlap(void);\n+\n+ int selectMethod(void);\n+\n+ void printSeqIdentity(void);\n+\n+ bool calculateSpuriousVector(float, float *);\n+\n+ void checkTypeAlignment(void);\n+\n+ int getTypeAlignment(void);\n+\n+ int *getCorrespResidues(void);\n+\n+ int *getCorrespSequences(void);\n+\n+ bool isFileAligned(void);\n+\n+ alignment * getTranslationCDS(int, int, int *, string *, sequencesMatrix *, alignment *);\n+\n+ bool checkCorrespondence(string *, int *, int, int);\n+\n+ int *calculateRepresentativeSeq(float maximumIdent);\n+\n+ /* New code: version 1.4 */\n+\n+ void computeComplementaryAlig(bool, bool);\n+\n+ void removeSmallerBlocks(int);\n+\n+ bool removeOnlyTerminal(void);\n+\n+ bool removeOnlyTerminal(int, int);\n+\n+ newValues removeCols_SeqsAllGaps(void);\n+\n+ void removeCols_SeqsAllGaps(newValues *);\n+\n+ void fillNewDataStructure(string *, string *);\n+ void fillNewDataStructure(newValues *);\n+\n+ // New Code: February/2012\n+ void calculateColIdentity(float *);\n+ void printColumnsIdentity_DescriptiveStats(void);\n+\n+ // New Code: May/2012\n+ void setKeepSequencesFlag(bool);\n+\n+ // New Code: Mar/2013\n+ void setKeepSeqsHeaderFlag(bool);\n+\n+ void printAlignmentInfo(ostream &);\n+\n+ // Updated: June/2013\n+ bool prepareCodingSequence(bool, bool, alignment *);\n+};\n+\n+#endif\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/autAlignment.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/autAlignment.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,448 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl.\n+\n+ trimAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+#include "alignment.h"\n+#include "defines.h"\n+\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+/* This function computes the identities values between the sequences from\n+ * the alignment */\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+void alignment::calculateSeqIdentity(void) {\n+\n+ int i, j, k, hit, dst;\n+ char indet;\n+\n+ /* Depending on alignment type, indetermination symbol will be one or other */\n+ indet = getTypeAlignment() == AAType ? \'X\' : \'N\';\n+\n+ /* Create identities matrix to store identities scores */\n+ identities = new float*[sequenNumber];\n+\n+ /* For each seq, compute its identity score against the others in the MSA */\n+ for(i = 0; i < sequenNumber; i++) {\n+ identities[i] = new float[sequenNumber];\n+\n+ /* It\'s a symmetric matrix, copy values that have been already computed */\n+ for(j = 0; j < i; j++)\n+ identities[i][j] = identities[j][i];\n+ identities[i][i] = 0;\n+\n+ /* Compute identity scores for the current sequence against the rest */\n+ for(j = i + 1; j < sequenNumber; j++) {\n+ for(k = 0, hit = 0, dst = 0; k < residNumber; k++) {\n+ /* If one of the two positions is a valid residue,\n+ * count it for the common length */\n+ if(((sequences[i][k] != indet) && (sequences[i][k] != \'-\')) ||\n+ ((sequences[j][k] != indet) && (sequences[j][k] != \'-\'))) {\n+ dst++;\n+ /* If both positions are the same, count a hit */\n+ if(sequences[i][k] == sequences[j][k])\n+ hit++;\n+ }\n+ }\n+\n+ /* Identity score between two sequences is the ratio of identical residues\n+ * by the total length (common and no-common residues) among them */\n+ identities[i][j] = (float) hit/dst;\n+ }\n+ }\n+}\n+\n+void alignment::calculateSeqOverlap(void) {\n+ /* Compute the overlap between sequences taken each of them as the reference\n+ * to compute such scores. It will lead to a non-symmetric matrix. */\n+\n+ int i, j, k, shared, referenceLength;\n+ char indet;\n+\n+ /* Depending on alignment type, indetermination symbol will be one or other */\n+ indet = getTypeAlignment() == AAType ? \'X\' : \'N\';\n+\n+ /* Create overlap matrix to store overlap scores */\n+ overlaps = new float*[sequenNumber];\n+\n+ /* For each seq, compute its overlap score against the others in the MSA */\n+ for(i = 0; i < sequenNumber; i++) {\n+ overlaps[i] = new float[sequenNumber];\n+\n+ for(j = 0; j < sequenNumber; j++) {\n+ for(k = 0, shared = 0, referenceLength = 0; k < residNumber; k++) {\n+ /* If there a valid residue for the reference sequence, then see if\n+ * there is a valid residue for the other sequence. */\n+ if((sequences[i][k] != indet) && (sequences[i][k] != \'-\')) {\n+ referenceL'..b'\n+ cout.precision(4);\n+ cout << fixed;\n+\n+ for(i = 0, maxSeq = 0; i < sequenNumber; i++)\n+ if(maxs[i][0] > maxSeq)\n+ maxSeq = maxs[i][0];\n+\n+ cout << "## MaxOverlap\\t" << maxSeq;\n+ cout << endl << "#> MaxOverlap\\tGet the maximum overlap value for any pair "\n+ << "of sequences in the alignment" << endl;\n+\n+ cout << endl << "## AverageOverlap\\t" << avgSeq;\n+ cout << endl << "#> AverageOverlap\\tAverage overlap between all sequences";\n+\n+ cout << endl << endl << "## Overlap sequences matrix";\n+ for(i = 0; i < sequenNumber; i++) {\n+ cout << endl << setw(maxLongName + 2) << left << seqsName[i] << "\\t";\n+ for(j = 0; j < sequenNumber; j++)\n+ cout << setiosflags(ios::left) << setw(10) << overlaps[i][j] << "\\t";\n+ }\n+ cout << endl;\n+}\n+\n+/* *** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *** */\n+/* */\n+/* NEW CODE: feb/2012 */\n+/* */\n+/* *** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *** */\n+void alignment::calculateColIdentity(float *ColumnIdentities) {\n+\n+ int i, j, counter, pos, max, columnLen;\n+ char letter, indet, gapSymbol;\n+ string column;\n+\n+ /* Initialize some data for make computation more precise */\n+ indet = getTypeAlignment() == AAType ? \'X\' : \'N\';\n+ gapSymbol = \'-\';\n+\n+ /* Compute identity score for the most frequent residue, it can be as well\n+ * gaps and indeterminations, for each column */\n+ for(i = 0, max = 0; i < residNumber; i++, max = 0, column.clear()) {\n+\n+ /* Get residues from each column in capital letters */\n+ for(j = 0; j < sequenNumber; j++)\n+ /* Discard gaps and indeterminations from calculations */\n+ if((toupper(sequences[j][i]) != indet) && (sequences[j][i] != gapSymbol))\n+ column += toupper(sequences[j][i]);\n+ columnLen = column.size();\n+\n+ /* Count letter frequency. It only matter the frequency. Use some shorcuts\n+ * to speed-up the process */\n+ while (!column.empty()) {\n+ letter = column[0];\n+ counter = 0;\n+ pos = 0;\n+\n+ do {\n+ counter += 1;\n+ column.erase(pos, 1);\n+ pos = column.find(letter, pos);\n+ } while(pos != (int) string::npos);\n+\n+ /* Keep only the most frequent residue */\n+ if(counter > max)\n+ max = counter;\n+ /* If column size is smaller than the current max, stop the count */\n+ if((int) column.size() < max)\n+ break;\n+ }\n+\n+ /* Store column identity values */\n+ if(columnLen != 0)\n+ ColumnIdentities[i] = float(max)/columnLen;\n+ }\n+}\n+\n+void alignment::printColumnsIdentity_DescriptiveStats(void) {\n+\n+ float *colIdentities, avg, std, max, min;\n+ int i, positions;\n+\n+ /* Allocate local memory for the computation */\n+ colIdentities = new float[residNumber];\n+\n+ utils::initlVect(colIdentities, residNumber, -1);\n+ calculateColIdentity(colIdentities);\n+\n+ for(i = 0, max = 0, min = 1, avg = 0, positions = 0; i < residNumber; i++) {\n+ if(colIdentities[i] != -1) {\n+ /* Compute on-the-fly max and min scores. Store accumulative score */\n+ avg += colIdentities[i];\n+ max = (colIdentities[i] > max) ? colIdentities[i] : max;\n+ min = (colIdentities[i] < min) ? colIdentities[i] : min;\n+ /* Count how many columns have a value score */\n+ positions += 1;\n+ }\n+ }\n+ /* Compute average identity column score */\n+ avg /= positions;\n+\n+ /* Compute standard desviation */\n+ for(i = 0, std = 0; i < residNumber; i++)\n+ if(colIdentities[i] != -1)\n+ std += pow((colIdentities[i] - avg), 2);\n+ std = sqrt(std/positions);\n+\n+ /* Print general descriptive stats */\n+ cout << "#maxColIdentity\\t" << max << endl;\n+ cout << "#minColIdentity\\t" << min << endl;\n+ cout << "#avgColIdentity\\t" << avg << endl;\n+ cout << "#stdColIdentity\\t" << std << endl;\n+}\n+\n+\n+\n+\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/compareFiles.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/compareFiles.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,518 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl.\n+\n+ trimAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include "compareFiles.h"\n+#include "alignment.h"\n+\n+#define LONG 80\n+\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+/* This method compares a set of alignment in order to select the most\n+ * consistent one respect of the other ones. To compute the consistency\n+ * values we use the proportion of residue pairs per column in the aligs\n+ * to compare */\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+int compareFiles::algorithm(alignment **vectAlignments, char **fileNames, float *columnsValue, int numAlignments, bool verbosity) {\n+\n+ int *numResiduesAlig, *correspNames, *columnSeqMatrix, *columnSeqMatrixAux;\n+ int i, j, k, l, m, numSeqs, pairRes, hits, alig = 0;\n+ float max = 0, value = 0, **vectHits;\n+ bool appearErrors = false;\n+ string *names;\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Get some parameters from the alignment that has\n+ * been selected */\n+ numSeqs = vectAlignments[0] -> getNumSpecies();\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Allocate dinamic local memory */\n+ names = new string[numSeqs];\n+ correspNames = new int[numSeqs];\n+ numResiduesAlig = new int[numAlignments];\n+ columnSeqMatrix = new int[numSeqs];\n+ vectHits = new float*[numAlignments];\n+ columnSeqMatrixAux = new int[numSeqs];\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Check that all of alignment has the same number of\n+ * sequence as well as there exists a correspondence\n+ * between the names for each pars of aligs. */\n+ for(i = 1; i < numAlignments; i++) {\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ if(numSeqs != vectAlignments[i] -> getNumSpecies()) {\n+ cerr << endl << "ERROR: The files to compare do not have "\n+ << "the same number of sequences" << endl << endl;\n+ appearErrors = true;\n+ break;\n+ }\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ vectAlignments[i] -> getSequences(names);\n+ if(!vectAlignments[0] -> getSeqNameOrder(names, correspNames)) {\n+ cerr << endl << "ERROR: The files to compare do not"\n+ << " have the sequence names" << endl << endl;\n+ appearErrors = true;\n+ break;\n+ }\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ }\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Changes the order in sequences number matrix\n+ * according to the order in the selected alignment */\n+ for(i = 1; ((i < numAlignments) && (!appearErrors)); i++) {\n+ vectAlignments[i] -> getSequences(names);\n+ vectAlignments[0] -> getSeqNameO'..b'* ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* If everything is OK, return true */\n+ return true;\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+}\n+\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+/* Print the consistency value for each column from the selected alignment */\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+void compareFiles::printStatisticsFileColumns(int numAminos, float *compareVect) {\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Prepare the header information */\n+ cout << "| Residue\\tConsistency |" << endl;\n+ cout << "| Number \\t Value |" << endl;\n+ cout << "+---------------------------+" << endl;\n+ cout.precision(10);\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Print the consistency values for each column from\n+ * the selected alignment */\n+ for(int i = 0; i < numAminos; i++)\n+ cout << " " << setw(5) << i + 1 << "\\t"\n+\t << "\\t" << compareVect[i] << endl;\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+}\n+\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+/* Print the consistency values accumulative distribution for the selected\n+ * alignment */\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+void compareFiles::printStatisticsFileAcl(int numAminos, float *compareVect) {\n+\n+ float refer, *vectAux;\n+ int i, num;\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Allocate dinamic memory to copy the input vector\n+ * and sort it */\n+ vectAux = new float[numAminos];\n+ utils::copyVect(compareVect, vectAux, numAminos);\n+ utils::quicksort(vectAux, 0, numAminos-1);\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Set the output precision and print the header */\n+ cout << "| Number of\\t \\t|\\t Cumulative \\t% "\n+ << "Cumulative\\t| Consistency |" << endl;\n+ cout << "| Residues \\t% Length\\t|\\tNumberResid.\\t "\n+ << "Length \\t| Value |" << endl;\n+ cout << "+-------------------------------+------------"\n+ << "---------------------------+-----------------+"\n+\t << endl;\n+ cout.precision(10);\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Fix the initial values to count how many columns\n+ * has the same consistency value */\n+ refer = vectAux[0];\n+ num = 1;\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Print the accumulative distribution */\n+ for(i = 1; i < numAminos; i++) {\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\t/* When the method detects a new consistency value\n+\t * print the previous value as well as its frequency\n+\t * and starts to count how many columns are for this\n+\t * new value */\n+ if(refer != vectAux[i]) {\n+ cout << " " << num << "\\t\\t" << setw(10) << ((float) num/numAminos * 100.0)\n+ << "\\t\\t" << i << "\\t\\t" << setw(10) << ((float) i/numAminos * 100.0)\n+ << "\\t" << setw(15) << refer << endl;\n+ refer = vectAux[i];\n+ num = 1;\n+ }\n+ else num++;\n+\t/* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ }\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Print the last consistency value as well as its\n+ * frequency */\n+ cout << " " << num << "\\t\\t" << setw(10) << ((float) num/numAminos * 100.0)\n+ << "\\t\\t" << i << "\\t\\t" << setw(10) << ((float) i/numAminos * 100.0)\n+\t << "\\t" << setw(15) << refer << endl;\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* Deallocate dinamic memory */\n+ delete [] vectAux;\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** */\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/compareFiles.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/compareFiles.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,51 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef COMPAREFILES_H
+#define COMPAREFILES_H
+
+#include <stdlib.h>
+
+#include <string>
+#include <iostream>
+
+#include "alignment.h"
+
+class compareFiles {
+
+ public:
+
+ static void printStatisticsFileColumns(int, float *);
+
+ static void printStatisticsFileAcl(int, float *);
+
+ static bool applyWindow(int, int, float *);
+
+ static int algorithm(alignment **, char **, float *, int, bool);
+
+ static bool forceComparison(alignment **, int, alignment *, float *);
+};
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/defines.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/defines.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,54 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ readAl v1.4: a tool for automated alignment conversion among different
+ formats.
+
+ statAl v1.4: a tool for getting descriptive alignment features/scores.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl/readAl.
+
+ trimAl/readAl are free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl/readAl are distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#define BUILD "2015-05-21"
+#define VERSION 1.4
+#define REVISION 22
+#define AUTHORS "2009-2015. Salvador Capella-Gutierrez and Toni Gabaldón."
+
+#define DNAType 1
+#define RNAType 2
+#define AAType 3
+#define DNADeg 4
+#define RNADeg 5
+
+#define SINGLE 1
+#define MULTI 2
+
+#define GAPPYOUT 1
+#define STRICT 2
+
+#define DELIMITERS " \t\n"
+#define OTHDELIMITERS " \t\n,:"
+#define OTH2DELIMITERS " \n,:;"
+
+#define HTMLBLOCKS 120
+#define PHYLIPDISTANCE 10

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/main.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/main.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,1973 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl.\n+\n+ trimAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include <fstream>\n+#include <iostream>\n+#include <iomanip>\n+\n+#include <stdlib.h>\n+#include <string.h>\n+\n+#include "compareFiles.h"\n+#include "compareFiles.h"\n+#include "alignment.h"\n+#include "defines.h"\n+#include "utils.h"\n+\n+void menu(void);\n+void examples(void);\n+\n+int main(int argc, char *argv[]){\n+\n+ /* Parameters Control */\n+ bool appearErrors = false, complementary = false, colnumbering = false, nogaps = false, noallgaps = false, gappyout = false,\n+ strict = false, strictplus = false, automated1 = false, sgc = false, sgt = false, scc = false, sct = false, sfc = false,\n+ sft = false, sident = false, soverlap = false, selectSeqs = false, selectCols = false, shortNames = false, splitbystop = false,\n+ terminal = false, keepSeqs = false, keepHeader = false, ignorestop = false;\n+\n+ float conserve = -1, gapThreshold = -1, simThreshold = -1, comThreshold = -1, resOverlap = -1, seqOverlap = -1, maxIdentity = -1;\n+\n+ int outformat = -1, compareset = -1, stats = 0, windowSize = -1, gapWindow = -1, simWindow = -1, conWindow = -1,\n+ blockSize = -1, clusters = -1, alternative_matrix = -1, alignDataType = -1;\n+\n+ /* Others varibles */\n+ ifstream compare;\n+ float *compareVect = NULL;\n+ alignment **compAlig = NULL;\n+ string nline, *seqNames = NULL;\n+ sequencesMatrix *seqMatrix = NULL;\n+ similarityMatrix *similMatrix = NULL;\n+ alignment *origAlig = NULL, *intermediateAlig = NULL, *singleAlig = NULL, *backtranslation = NULL;\n+\n+ int i = 1, lng, num = 0, maxAminos = 0, numfiles = 0, referFile = 0, *delColumns = NULL, *delSequences = NULL, *seqLengths = NULL, *boundaries = NULL;\n+ char c, *forceFile = NULL, *infile = NULL, *backtransFile = NULL, *outfile = NULL, *outhtml = NULL, *matrix = NULL,\n+ **filesToCompare = NULL, line[256];\n+\n+ /* ------------------------------------------------------------------------------------------------------ */\n+\n+ /* Exec: TrimAl - Shows the menu. */\n+\n+ /* ------------------------------------------------------------------------------------------------------ */\n+ if(argc == 1) {\n+ menu();\n+ return 0;\n+ }\n+\n+ /* ------------------------------------------------------------------------------------------------------ */\n+\n+ /* Help and Version Menu */\n+\n+ /* ------------------------------------------------------------------------------------------------------ */\n+ if(!strcmp(argv[i], "-h") && (i+1 == argc)) {\n+ menu(); examples();\n+ return 0;\n+ }\n+\n+ if(!strcmp(argv[i], "--version") && (i+1 == argc)) {\n+ cout << endl << "trimAl v" << VERSION << ".rev" << REVISION\n+ << " build[" << BUILD << "]" << endl << endl;\n+ return 0;\n+ }\n+\n+ /***** ***** ***** ***** ***** ***** ***** Pa'..b'\n+\n+ cout << " -sgc " << "Print gap scores for each column in the input alignment." << endl;\n+ cout << " -sgt " << "Print accumulated gap scores for the input alignment." << endl;\n+ cout << " -ssc " << "Print similarity scores for each column in the input alignment." << endl;\n+ cout << " -sst " << "Print accumulated similarity scores for the input alignment." << endl;\n+ cout << " -sfc " << "Print sum-of-pairs scores for each column from the selected alignment"\n+ << endl;\n+ cout << " -sft " << "Print accumulated sum-of-pairs scores for the selected alignment"\n+ << endl;\n+ cout << " -sident " << "Print identity scores matrix for all sequences in the input alignment. (see User Guide)."\n+ << endl;\n+ cout << " -soverlap " << "Print overlap scores matrix for all sequences in the input alignment. (see User Guide)."\n+ << endl << endl;\n+}\n+\n+void examples(void) {\n+\n+ cout << "Some Examples:" << endl << endl;\n+\n+ cout << "1) Removes all positions in the alignment with gaps in 10% or more of" << endl\n+ << " the sequences, unless this leaves less than 60% of original alignment. " << endl\n+ << " In such case, print the 60% best (with less gaps) positions." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60" << endl << endl;\n+\n+ cout << "2) As above but, the gap score is averaged over a window starting" << endl\n+ << " 3 positions before and ending 3 positions after each column." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60 -w 3" << endl << endl;\n+\n+ cout << "3) Use an automatic method to decide optimal thresholds, based in the gap scores" << endl\n+ << " from input alignment. (see User Guide for details)." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -gappyout" << endl << endl;\n+\n+ cout << "4) Use automatic methods to decide optimal thresholds, based on the combination " << endl\n+ << " of gap and similarity scores. (see User Guide for details)." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -strictplus" << endl << endl;\n+\n+ cout << "5) Use an heuristic to decide the optimal method for trimming the alignment. " << endl\n+ << " (see User Guide for details)." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -automated1" << endl << endl;\n+\n+ cout << "6) Use residues and sequences overlap thresholds to delete some sequences from the " << endl\n+ << " alignemnt. (see User Guide for details)." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -resoverlap 0.8 -seqoverlap 75" << endl << endl;\n+\n+ cout << "7) Selection of columns to be deleted from the alignment. The selection can " << endl\n+ << " be a column number or a column number interval. Start from 0" << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 }" << endl << endl;\n+\n+ cout << "8) Get the complementary alignment from the alignment previously trimmed." << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 } -complementary" << endl << endl;\n+\n+ cout << "9) Selection of sequences to be deleted from the alignment. Start in 0" << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -selectseqs { 2,4,8-12 } " << endl << endl;\n+\n+ cout << "10) Select the 5 most representative sequences from the alignment" << endl << endl;\n+\n+ cout << " trimal -in <inputfile> -out <outputfile> -clusters 5 " << endl << endl;\n+}\n+\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/makefile Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,50 @@
+CODE  = main.cpp
+NAME  = trimal
+
+CODE2 = readAl.cpp
+NAME2 = readal
+
+CODE3 = statAl.cpp
+NAME3 = statal
+
+CC    = g++
+FLAGS = -Wall -O2
+LIBM  = -lm
+DUGB  =
+
+all: readal trimal statal
+
+preview: alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+trimal: preview
+ $(CC) $(FLAGS) $(DUGB) -o $(NAME) $(CODE) $(LIBM) alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+readal: preview
+ $(CC) $(FLAGS) $(DUGB) -o $(NAME2) $(CODE2) $(LIBM) alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+statal: preview
+ $(CC) $(FLAGS) $(DUGB) -o $(NAME3) $(CODE3) $(LIBM) alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+alignment.o: alignment.cpp rwAlignment.cpp autAlignment.cpp alignment.h values.h defines.h
+ $(CC) $(FLAGS) $(DUGB) -c alignment.cpp rwAlignment.cpp autAlignment.cpp
+
+statisticsGaps.o: statisticsGaps.cpp statisticsGaps.h
+ $(CC) $(FLAGS) $(DUGB) -c statisticsGaps.cpp
+
+sequencesMatrix.o: sequencesMatrix.cpp sequencesMatrix.h
+ $(CC) $(FLAGS) $(DUGB) -c sequencesMatrix.cpp
+
+statisticsConservation.o: statisticsConservation.cpp statisticsConservation.h
+ $(CC) $(FLAGS) $(DUGB) -c statisticsConservation.cpp
+
+similarityMatrix.o: similarityMatrix.cpp similarityMatrix.h values.h
+ $(CC) $(FLAGS) $(DUGB) -c similarityMatrix.cpp
+
+utils.o: utils.cpp utils.h values.h  defines.h
+ $(CC) $(FLAGS) $(DUGB) -c utils.cpp
+
+compareFiles.o: compareFiles.cpp compareFiles.h
+ $(CC) $(FLAGS) $(DUGB) -c compareFiles.cpp
+
+clean:
+ -rm -f $(NAME) $(NAME2)  $(NAME3) *.o *~

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/makefile.MacOS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/makefile.MacOS Fri Mar 25 17:10:43 2022 +0000

@@ -0,0 +1,53 @@
+## Substitute generic 'makefile' file for this one
+## some flags on the official makefile make it difficult for compilers on MacOS architecture.
+
+CODE  = main.cpp
+NAME  = trimal
+
+CODE2 = readAl.cpp
+NAME2 = readal
+
+CODE3 = statAl.cpp
+NAME3 = statal
+
+CC    = g++
+FLAGS = -Wall
+LIBM  = -lm
+DUGB  =
+
+all: readal trimal statal
+
+preview: alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+trimal: preview
+ $(CC) $(FLAGS) $(DUGB) -o $(NAME) $(CODE) $(LIBM) alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+readal: preview
+ $(CC) $(FLAGS) $(DUGB) -o $(NAME2) $(CODE2) $(LIBM) alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+statal: preview
+ $(CC) $(FLAGS) $(DUGB) -o $(NAME3) $(CODE3) $(LIBM) alignment.o statisticsGaps.o utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o
+
+alignment.o: alignment.cpp rwAlignment.cpp autAlignment.cpp alignment.h values.h defines.h
+ $(CC) $(FLAGS) $(DUGB) -c alignment.cpp rwAlignment.cpp autAlignment.cpp
+
+statisticsGaps.o: statisticsGaps.cpp statisticsGaps.h
+ $(CC) $(FLAGS) $(DUGB) -c statisticsGaps.cpp
+
+sequencesMatrix.o: sequencesMatrix.cpp sequencesMatrix.h
+ $(CC) $(FLAGS) $(DUGB) -c sequencesMatrix.cpp
+
+statisticsConservation.o: statisticsConservation.cpp statisticsConservation.h
+ $(CC) $(FLAGS) $(DUGB) -c statisticsConservation.cpp
+
+similarityMatrix.o: similarityMatrix.cpp similarityMatrix.h values.h
+ $(CC) $(FLAGS) $(DUGB) -c similarityMatrix.cpp
+
+utils.o: utils.cpp utils.h values.h  defines.h
+ $(CC) $(FLAGS) $(DUGB) -c utils.cpp
+
+compareFiles.o: compareFiles.cpp compareFiles.h
+ $(CC) $(FLAGS) $(DUGB) -c compareFiles.cpp
+
+clean:
+ -rm -f $(NAME) $(NAME2)  $(NAME3) *.o *~

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/readAl.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/readAl.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,383 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ readAl v1.4: a tool for automated alignment conversion among different\n+ formats.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of readAl.\n+\n+ readAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ readAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with readAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include <stdlib.h>\n+#include <string.h>\n+\n+#include "alignment.h"\n+#include "defines.h"\n+#include "utils.h"\n+\n+void menu(void);\n+\n+int main(int argc, char *argv[]) {\n+\n+ /* Input alignment */\n+ alignment inAlig;\n+\n+ /* Local variables */\n+ string align_format;\n+ int i, outformat = -1;\n+ char *infile = NULL, *outfile = NULL;\n+ bool errors = false, reverse = false, shortNames = false, format = false, \\\n+ type = false, info = false;\n+\n+ /* If there is no parameters: Inform about readAl options and finish */\n+ if(argc == 1) {\n+ menu();\n+ return 0;\n+ }\n+\n+ i = 1;\n+ /* If option -h has been used, inform about readAl options and finish */\n+ if(!strcmp(argv[i], "-h") && (i+1 == argc)) {\n+ menu();\n+ return 0;\n+ }\n+\n+ /* Inform about current readAl version/revision/build and finish */\n+ if(!strcmp(argv[i], "--version") && (i+1 == argc)) {\n+ cout << endl << "readAl v" << VERSION << ".rev" << REVISION << " build["\n+ << BUILD << "]" << endl << endl;\n+ return 0;\n+ }\n+\n+ /* Catch different input options and then check whether there is a valid\n+ * combination of parameters */\n+ while(i < argc) {\n+\n+ /* Input alignment option: -in */\n+ if(!strcmp(argv[i], "-in") && (i+1 != argc) && (infile == NULL)) {\n+ /* Allocate memory for storing input alignment filename */\n+ infile = new char[strlen(argv[++i]) + 1];\n+ strcpy(infile, argv[i]);\n+\n+ /* Load input alignment and inform about it if something is wrong */\n+ if(!inAlig.loadAlignment(infile)) {\n+ cerr << endl << "ERROR: Alignment not loaded: \\"" << infile\n+ << "\\" Check the file\'s content." << endl << endl;\n+ errors = true;\n+ }\n+ }\n+\n+ /* Output filename option: -out */\n+ else if(!strcmp(argv[i], "-out") && (i+1 != argc) && (outfile == NULL)) {\n+ /* Allocate memory for storing output alignment filename */\n+ outfile = new char[strlen(argv[++i]) + 1];\n+ strcpy(outfile, argv[i]);\n+ }\n+\n+ /* Get information about input file format */\n+ else if(!strcmp(argv[i], "-format") && (!format))\n+ format = true;\n+\n+ /* Get information about input file residues type */\n+ else if(!strcmp(argv[i], "-type") && (!type))\n+ type = true;\n+\n+ /* Get general information about input file: seqs number, average seq length,\n+ * etc */\n+ else if(!strcmp(argv[i], "-info") && (!info))\n+ info = true;\n+\n+ /* Get input sequences reverse option: -reverse */\n+ else if(!strcmp(argv[i], "-reverse") && (!reverse))\n+ reverse = true;\n+\n+ /* For all output format options is checked if more\n+ * than one output format has been required */\n+\n+ /* Set output alignment format to CLUSTAL: -clustal */\n+ else if(!strcmp(argv[i], "-clustal") && (outformat == -1))\n+ outformat = 1;\n+\n+ '..b'<< endl;\n+ }\n+\n+ if(info)\n+ inAlig.printAlignmentInfo(cout);\n+ }\n+\n+ if((outfile != NULL) || (outformat != -1) || reverse || shortNames) {\n+ /* Set output format */\n+ if(outformat != -1 || shortNames)\n+ inAlig.setOutputFormat(outformat, shortNames);\n+ /* Ask for getting the reverse of input file */\n+ if(reverse)\n+ inAlig.setReverse();\n+\n+ /* If a outfile has been provided, try to generate output file */\n+ if(outfile != NULL) {\n+ if(!inAlig.saveAlignment(outfile)) {\n+ cerr << endl << "ERROR: Impossible to generate OUTPUT file." << endl\n+ << endl;\n+ return -1;\n+ }\n+ /* ... otherwise dump outfile content to standard output */\n+ } else {\n+ inAlig.printAlignment();\n+ }\n+ }\n+ }\n+\n+ /* Deallocate local memory */\n+ delete [] infile;\n+ delete [] outfile;\n+\n+ /* Inform about readAl execution */\n+ return (errors == true ? -1 : 0);\n+}\n+\n+void menu(void) {\n+\n+ cout << endl\n+ << "readAl v" << VERSION << ".rev" << REVISION << " build[" << BUILD\n+ << "]. " << AUTHORS << endl << endl\n+\n+ << "readAl webpage: http://trimal.cgenomics.org" << endl << endl\n+\n+ << "This program is free software: you can redistribute it and/or modify "\n+ << endl\n+ << "it under the terms of the GNU General Public License as published by "\n+ << endl\n+ << "the Free Software Foundation, the last available version." << endl\n+ << endl\n+\n+ << "Basic usage" << endl\n+ << "\\treadal -in <inputfile> -out <outputfile> [options]." << endl << endl\n+\n+ << "\\t-h " << "Show this information." << endl\n+ << "\\t--version " << "Show readAl version." << endl << endl\n+\n+ << "\\t-in <inputfile> " << "Input file in several formats." << endl\n+ << "\\t-out <outputfile> " << "Output file name (default STDOUT)." << endl\n+ << endl\n+\n+ << "\\t-format " << "Print information about input file format "\n+ << "and if sequences are aligned or not." << endl\n+\n+ << "\\t-type " << "Print information about biological "\n+ << "sequences datatype (e.g. nucleotides:dna, nucleotides:rna, aminoacids, etc)"\n+ << endl\n+\n+ << "\\t-info " << "Print information about sequences number, "\n+ << "average sequence length, max & min sequence length"\n+ << endl << endl\n+\n+ << "\\t-onlyseqs " << "Generate output with only residues from "\n+ << "input file" << endl << endl\n+\n+ << "\\t-html " << "Output residues colored according their "\n+ << "physicochemical properties. HTML file." << endl << endl\n+\n+ << "\\t-reverse " << "Output the reverse of sequences in "\n+ << "input file." << endl << endl\n+\n+ << "\\t-nbrf " << "Output file in NBRF/PIR format" << endl\n+ << "\\t-mega " << "Output file in MEGA format" << endl\n+\n+ << "\\t-nexus " << "Output file in NEXUS format" << endl\n+ << "\\t-clustal " << "Output file in CLUSTAL format" << endl\n+ << endl\n+\n+ << "\\t-fasta " << "Output file in FASTA format" << endl\n+ << "\\t-fasta_m10 " << "Output file in FASTA format. Sequences "\n+ << "name up to 10 characters." << endl << endl\n+\n+ << "\\t-phylip " << "Output file in PHYLIP/PHYLIP4 format"\n+ << endl\n+ << "\\t-phylip_m10 " << "Output file in PHYLIP/PHYLIP4 format. "\n+ << "Sequences name up to 10 characters." << endl\n+ << "\\t-phylip_paml " << "Output file in PHYLIP format compatible "\n+ << "with PAML" << endl\n+ << "\\t-phylip_paml_m10 " << "Output file in PHYLIP format compatible "\n+ << "with PAML. Sequences name up to 10 characters." << endl\n+ << "\\t-phylip3.2 " << "Output file in PHYLIP3.2 format" << endl\n+ << "\\t-phylip3.2_m10 " << "Output file in PHYLIP3.2 format. Sequences"\n+ << " name up to 10 characters." << endl << endl;\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/rwAlignment.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/rwAlignment.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,2253 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ readAl v1.4: a tool for automated alignment conversion among different\n+ formats.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl/readAl.\n+\n+ trimAl/readAl are free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl/readAl are distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include "alignment.h"\n+#include "defines.h"\n+#include "utils.h"\n+\n+extern int errno;\n+#include <errno.h>\n+#include <ctype.h>\n+#include <string>\n+\n+using namespace std;\n+\n+bool alignment::fillMatrices(bool aligned) {\n+ /* Function to determine if a set of sequences, that can be aligned or not,\n+ * have been correctly load and are free of errors. */\n+ int i, j;\n+\n+ /* Initialize some variables */\n+ residuesNumber = new int[sequenNumber];\n+ for(i = 0; i < sequenNumber; i++) {\n+ residuesNumber[i] = sequences[i].size();\n+ }\n+\n+ /* Check whether there are any unknow/no allowed character in the sequences */\n+ for(i = 0; i < sequenNumber; i++)\n+ for(j = 0; j < residuesNumber[i]; j++)\n+ if((!isalpha(sequences[i][j])) && (!ispunct(sequences[i][j]))) {\n+ cerr << endl << "ERROR: The sequence \\"" << seqsName[i] << "\\" has an "\n+ << "unknown (" << sequences[i][j] << ") character." << endl;\n+ return false;\n+ }\n+\n+ /* Check whether all sequences have same size or not */\n+ for(i = 1; i < sequenNumber; i++)\n+ if(residuesNumber[i] != residuesNumber[i-1])\n+ break;\n+ /* Set an appropriate flag for indicating if sequences are aligned or not */\n+ isAligned = (i != sequenNumber) ? false : true;\n+\n+ /* Warm about those cases where sequences should be aligned\n+ * and there are not */\n+ if (aligned and !isAligned) {\n+ cerr << endl << "ERROR: Sequences should be aligned (all with same length) "\n+ << "and there are not. Check your input alignment" << endl;\n+ return false;\n+ }\n+\n+ /* Full-fill some information about input alignment */\n+ if(residNumber == 0)\n+ residNumber = residuesNumber[0];\n+\n+ /* Check whether aligned sequences have the length fixed for the input alig */\n+ for(i = 0; (i < sequenNumber) and (aligned); i++) {\n+ if(residuesNumber[i] != residNumber) {\n+ cerr << endl << "ERROR: The sequence \\"" << seqsName[i] << "\\" ("\n+ << residuesNumber[i] << ") does not have the same number of residues "\n+ << "fixed by the alignment (" << residNumber << ")." << endl;\n+ return false;\n+ }\n+ }\n+\n+ /* If the sequences are aligned, initialize some additional variables.\n+ * These variables will be useful for posterior analysis */\n+ if((aligned) || (isAligned)) {\n+\n+ /* Asign its position to each column. That will be used to determine which\n+ * columns should be kept in output alignment after applying any method\n+ * and which columns should not */\n+ saveResidues = new int[residNumber];\n+ for(i = 0; i < residNumber; i++)\n+ saveResidues[i] = i;\n+\n+ /* Asign its position to each sequence. Similar to the columns numb'..b'me = 0;\n+ for(i = 0; i < sequenNumber; i++)\n+ maxLongName = utils::max(maxLongName, seqsName[i].size());\n+\n+\n+ /* Print HTML header into output file */\n+ file << "<!DOCTYPE html>" << endl << "<html><head>" << endl << " <meta "\n+ << "http-equiv=\\"Content-Type\\" content=\\"text/html;charset=ISO-8859-1\\" />"\n+ << endl << " <title>readAl v1.4</title>" << endl\n+ << " <style type=\\"text/css\\">" << endl\n+ << " #b { background-color: #3366ff; }\\n"\n+ << " #r { background-color: #cc0000; }\\n"\n+ << " #g { background-color: #33cc00; }\\n"\n+ << " #p { background-color: #ff6666; }\\n"\n+ << " #m { background-color: #cc33cc; }\\n"\n+ << " #o { background-color: #ff9900; }\\n"\n+ << " #c { background-color: #46C7C7; }\\n"\n+ << " #y { background-color: #FFFF00; }\\n"\n+ << " </style>\\n </head>\\n\\n" << " <body>\\n <pre>" << endl;\n+\n+ /* Print sequences colored according to CLUSTAL scheme based on\n+ * physical-chemical properties */\n+ for(j = 0, upper = HTMLBLOCKS; j < residNumber; j += HTMLBLOCKS, upper += \\\n+ HTMLBLOCKS) {\n+\n+ file << endl;\n+ /* Print main columns number */\n+ file << setw(maxLongName + 19) << right << (j + 10);\n+ for(i = j + 20; ((i <= residNumber) && (i <= upper)); i += 10)\n+ file << setw(10) << right << i;\n+\n+ /* Print special characters to delimit sequences blocks */\n+ file << endl << setw(maxLongName + 10);\n+ for(i = j + 1; ((i <= residNumber) && (i <= upper)); i++)\n+ file << (!(i % 10) ? "+" : "=");\n+\n+ /* Print sequences themselves */\n+ for(i = 0; i < sequenNumber; i++) {\n+\n+ /* Print sequences name */\n+ file << endl << setw(maxLongName + 9) << left << seqsName[i];\n+\n+ /* Print residues corresponding to current sequences block */\n+ for(k = j; ((k < residNumber) && (k < upper)); k++) {\n+ for(kj = 0, tmpColumn.clear(); kj < sequenNumber; kj++)\n+ tmpColumn += sequences[kj][k];\n+ /* Determine residue color based on residues across the alig column */\n+ type = utils::determineColor(sequences[i][k], tmpColumn);\n+ if (type == \'w\')\n+ file << sequences[i][k];\n+ else\n+ file << "" << sequences[i][k] << "";\n+ }\n+ }\n+ file << endl;\n+ }\n+\n+ /* Print HTML footer into output file */\n+ file << " </pre>" << endl << " </body>" << endl << "</html>" << endl;\n+\n+ return true;\n+}\n+\n+void alignment::printAlignmentInfo(ostream &file) {\n+ /* Print information about sequences number, average sequence length, maximum\n+ * and minimum sequences length, etc */\n+\n+ int i, j, valid_res, max, min, max_pos, min_pos, total_res;\n+\n+ /* Storage which sequences are the longest and shortest ones */\n+ max = 0;\n+ max_pos = 0;\n+ min_pos = 0;\n+ min = residuesNumber[0];\n+\n+ for(i = 0, total_res = 0; i < sequenNumber; i++) {\n+\n+ /* Discard gaps from current sequence and then compute real length */\n+ for(j = 0, valid_res = 0; j < residuesNumber[i]; j++)\n+ valid_res += (sequences[i][j] != \'-\' ? 1 : 0);\n+\n+ /* Compute the total residues in the alignment to calculate avg. sequence\n+ * length */\n+ total_res += valid_res;\n+\n+ /* Get values for the longest sequence */\n+ max_pos = (max > valid_res) ? max_pos : i;\n+ max = (max > valid_res) ? max : valid_res;\n+ /* Similarily, get values for the shortest sequence */\n+ min_pos = (min < valid_res) ? min_pos : i;\n+ min = (min < valid_res) ? min : valid_res;\n+ }\n+\n+ file << "## Total sequences\\t" << sequenNumber << endl;\n+ if (isFileAligned())\n+ file << "## Alignment length\\t" << residNumber << endl;\n+ file << "## Avg. sequence length\\t" << (float) total_res / sequenNumber << endl\n+ << "## Longest seq. name\\t\'" << seqsName[max_pos] << "\'" << endl\n+ << "## Longest seq. length\\t" << max << endl\n+ << "## Shortest seq. name\\t\'" << seqsName[min_pos] << "\'" << endl\n+ << "## Shortest seq. length\\t" << min << endl;\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/sequencesMatrix.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/sequencesMatrix.cpp Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,209 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#include "sequencesMatrix.h"
+
+sequencesMatrix::sequencesMatrix(void) {
+
+ resNumber = 0;
+ seqsNumber = 0;
+
+ seqsName = NULL;
+ matrix = NULL;
+
+}
+
+sequencesMatrix::sequencesMatrix(string *alignmentMatrix, string *alignmentSeqsName, int sequences, int residues) {
+ int i, j, k;
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ seqsNumber = sequences;
+ resNumber = residues;
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ seqsName = new string[seqsNumber];
+ for(i = 0; i < seqsNumber; i++)
+ seqsName[i] = alignmentSeqsName[i];
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ matrix = new int*[seqsNumber];
+ for(i = 0; i < seqsNumber; i++) {
+ matrix[i] = new int[resNumber];
+ utils::initlVect(matrix[i], resNumber, 0);
+ }
+
+ /* Determinate the sequence for each alignment specie */
+ for(i = 0, k = 1; i < seqsNumber; i++, k = 1) {
+ for(j = 0; j < resNumber; j++) {
+ if(alignmentMatrix[i][j] != '-') {
+ matrix[i][j] = k;
+ k++;
+ }
+ }
+ }
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+}
+
+sequencesMatrix &sequencesMatrix::operator=(const sequencesMatrix &old) {
+ int i, j;
+
+ if(this != &old) {
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ seqsNumber = old.seqsNumber;
+ resNumber = old.resNumber;
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ seqsName = new string[seqsNumber];
+ for(i = 0; i < seqsNumber; i++)
+ seqsName[i] = old.seqsName[i];
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ matrix = new int*[seqsNumber];
+ for(i = 0; i < seqsNumber; i++) {
+ matrix[i] = new int[resNumber];
+ for(j = 0; j < resNumber; j++)
+ matrix[i][j] = matrix[i][j];
+ }
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ }
+ return *this;
+}
+
+sequencesMatrix::~sequencesMatrix(void) {
+ int i;
+
+ if(matrix != NULL) {
+ for(i = 0; i < seqsNumber; i++)
+ delete matrix[i];
+ delete [] matrix;
+ }
+
+ if(seqsName != NULL)
+ delete [] seqsName;
+
+ seqsNumber = 0;
+ resNumber = 0;
+
+ matrix = NULL;
+ seqsName = NULL;
+}
+
+void sequencesMatrix::printMatrix(void) {
+ int i, j, k;
+
+ for(i = 0; i < resNumber; i += 20) {
+ for(j = 0; j < seqsNumber; j++) {
+ for(k = i; k < (20 + i) && k < resNumber; k++) {
+ cout << setw(4) << matrix[j][k] << " ";
+ }
+ cout << endl;
+ }
+ cout << endl;
+ }
+}
+
+void sequencesMatrix::getColumn(int column, int *columnSeqMatrix) {
+ int i;
+
+ if(column < resNumber)
+ for(i = 0; i < seqsNumber; i++)
+ columnSeqMatrix[i] = matrix[i][column];
+
+ else
+ for(i = 0; i < seqsNumber; i++)
+ columnSeqMatrix[i] = 0;
+
+}
+
+void sequencesMatrix::getColumn(int value, int row, int *columnSeqMatrix) {
+ int i, j;
+
+ for(i = 0; i < resNumber; i++)
+ if(matrix[row][i] == value) break;
+
+ if(i < resNumber)
+ for(j = 0; j < seqsNumber; j++)
+ columnSeqMatrix[j] = matrix[j][i];
+
+ else
+ for(j = 0; j < seqsNumber; j++)
+ columnSeqMatrix[j] = -1;
+}
+
+void sequencesMatrix::setOrder(int *order) {
+ int i, j, **resg;
+
+ resg = new int*[seqsNumber];
+ for(i = 0; i < seqsNumber; i++)
+ resg[i] = new int[resNumber];
+
+ for(i = 0; i < seqsNumber; i++)
+ for(j = 0; j < resNumber; j++)
+ resg[i][j] = matrix[order[i]][j];
+
+ for(i = 0; i < seqsNumber; i++) {
+ for(j = 0; j < resNumber; j++)
+ matrix[i][j] = resg[i][j];
+ delete [] resg[i];
+ }
+ delete [] resg;
+}
+
+bool sequencesMatrix::getSequence(string seqName, int *sequence) {
+ int i, pos;
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ for(pos = 0; pos < seqsNumber; pos++)
+ if(seqsName[pos].compare(seqName) == 0)
+ break;
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ if(pos == seqsNumber)
+ return false;
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+ for(i = 0; i < resNumber; i++)
+ sequence[i] = matrix[pos][i];
+ /* ***** ***** ***** ***** ***** ***** ***** ***** */
+
+ return true;
+}
+
+int sequencesMatrix::getSeqNumber(void) {
+ return seqsNumber;
+}
+
+int sequencesMatrix::getResidNumber(void) {
+ return resNumber;
+}
+
+

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/sequencesMatrix.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/sequencesMatrix.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,117 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef STATISTICSFILES_H
+#define STATISTICSFILES_H
+
+#include <iostream>
+#include <iomanip>
+
+#include "utils.h"
+
+using namespace std;
+
+/** \brief Class containing a sequences matrix
+ *
+ * This class stores the alignment sequences matrix. It provides
+ * methods to \b build the sequences matrix and print the matrix.
+ * It also provides methods for look to a column in the matrix and
+ * for look to value at the position (row, column) in the matrix.
+ */
+
+class sequencesMatrix {
+ int resNumber;
+ int seqsNumber;
+
+ /* Sequences Matrix */
+ int **matrix;
+
+ /* Sequences Name */
+ string *seqsName;
+
+ public:
+
+ /* Constructors */
+
+ /** \brief Null constructor.
+ *
+ * This construction method initializates all attributes
+ * of the new object with 0 or NULL value.
+ */
+ sequencesMatrix(void);
+
+ /* Copy constructor */
+ sequencesMatrix(string *, string *, int, int);
+
+ sequencesMatrix &operator=(const sequencesMatrix &);
+
+ /* Destructor */
+
+ /** \brief Destructor.
+ *
+ * Destruction method that frees, if exists, previously allocated memory.
+ */
+ ~sequencesMatrix();
+
+ /* Basics Operations. */
+
+ /** \brief Sequences Matrix printing method.
+ *
+ * Method that prints the alignment sequences matrix.
+ */
+ void printMatrix();
+
+ /** \brief Column for looking to method.
+ * \param column Column number at sequences matrix.
+ * \param numResidueseqMatrix Vector where storage a column's sequences matrix.
+ *
+ * Method that storages a column's sequences matrix in a vector.
+ */
+ void getColumn(int, int *);
+
+ /** \brief Column for looking to method.
+ * \param value to look in a row's sequences matrix.
+ * \param row where to look for a value.
+ * \param numResidueseqMatrix Vector where storage a column's sequences matrix.
+ *
+ * Method that looks to value in a row and storages a column's, corresponding to row,
+ * sequences matrix in a vector.
+ */
+ void getColumn(int, int, int *);
+
+ void setOrder(int *);
+
+ void removeColumns(int, int, int *, int *);
+
+ bool getSequence(string, int *);
+
+ int getSeqNumber(void);
+
+ int getResidNumber(void);
+
+};
+
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/similarityMatrix.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/similarityMatrix.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,463 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl.\n+\n+ trimAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#ifndef SIMMatrix\n+#define SIMMatrix\n+\n+#define NUMAMINOS 20\n+#define TAMABC 28\n+#define LINE_LENGTH 256\n+#define REFER 65\n+\n+#include "values.h"\n+#endif\n+\n+#include "similarityMatrix.h"\n+#include "utils.h"\n+\n+#include <iostream>\n+\n+#include <string.h>\n+#include <stdlib.h>\n+\n+using namespace std;\n+\n+extern char listSym[21];\n+extern float defaultMatrix[20][20];\n+\n+/*+++++++++++++++++++++++++++++++++++++++++++++\n+| similarityMatrix::similarityMatrix() |\n+| Class constructor. |\n++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+similarityMatrix::similarityMatrix(){\n+ numPositions = 0;\n+ vhash = NULL;\n+ simMat = NULL;\n+ distMat = NULL;\n+}\n+\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void similarityMatrix::memoryAllocation(int) |\n+| This method allocates memory for some class attributes |\n+| with a number of positios given as the method parameter |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void similarityMatrix::memoryAllocation(int nPos){\n+ int i, j;\n+\n+ /* Initializate square table dimension to store the distances */\n+ /* and to store the similarity matrix. */\n+ if(numPositions != 0) memoryDeletion();\n+ numPositions = nPos;\n+\n+ /* Reserve memory for all structures */\n+ vhash = new int[TAMABC];\n+\n+ simMat = new float *[nPos];\n+ distMat = new float *[nPos];\n+\n+ for(i = 0; i < nPos; i++) {\n+ simMat[i] = new float[nPos];\n+ distMat[i] = new float[nPos];\n+\n+ for(j = 0; j < nPos; j++) {\n+ distMat[i][j] = 0.0;\n+ simMat[i][j] = 0.0;\n+ }\n+ }\n+}\n+\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++\n+| similarityMatrix::~similarityMatrix() |\n+| Class destructor . |\n+++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+similarityMatrix::~similarityMatrix(){\n+\n+ if(numPositions != 0) memoryDeletion();\n+\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void similarityMatrix::memoryDeletion() |\n+| This method deletes all previously reserved memory |\n+| for the object attributes |\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void similarityMatrix::memoryDeletion(){\n+ int i;\n+\n+ for(i = 0; i < numPositions; i++){\n+ delete[] simMat[i]; delete[] distMat[i];\n+ }\n+\n+ delete[] simMat;\n+ delete[] distMat;\n+ delete[] vhash;\n+\n+ numPositions = 0;\n+ vhash = NULL;\n+ simMat = NULL;\n+ distMat = NULL;\n+}\n+\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| bool similarityMatrix::loadSimMatrix(char *) |\n+| This method loads a similarity matrix from a file |\n+| and checks if '..b'= 0; k < numPositions; k++)\n+ sum += ((simMat[k][j] - simMat[k][i]) * (simMat[k][j] - simMat[k][i]));\n+ sum = (float) sqrt(sum);\n+ distMat[i][j] = sum;\n+ distMat[j][i] = sum;\n+ }\n+ }\n+ }\n+}\n+\n+void similarityMatrix::alternativeSimilarityMatrices(int matrix_code, \\\n+ int datatype) {\n+ int i, j, k;\n+ float sum;\n+\n+ /* Allocate memory depending on the input datatype */\n+ switch(datatype) {\n+ case AAType:\n+ memoryAllocation(20);\n+ break;\n+ case DNAType:\n+ case RNAType:\n+ memoryAllocation(5);\n+ break;\n+ case DNADeg:\n+ case RNADeg:\n+ memoryAllocation(15);\n+ break;\n+ }\n+\n+ for(i = 0; i < TAMABC; i++)\n+ vhash[i] = -1;\n+\n+ /* We create the hashing vector taking into account the input datatype */\n+ for(i = 0; i < numPositions; i++) {\n+ switch(datatype) {\n+ case AAType:\n+ vhash[listAASym[i] - \'A\'] = i;\n+ break;\n+ case DNAType:\n+ case RNAType:\n+ vhash[listNTSym[i] - \'A\'] = i;\n+ break;\n+ case DNADeg:\n+ case RNADeg:\n+ vhash[listNTDegenerateSym[i] - \'A\'] = i;\n+ break;\n+ }\n+ }\n+\n+ /* Working similarity matrix is set depending on the preloaded matrices */\n+ for(i = 0; i < numPositions; i++) {\n+ for(j = 0; j < numPositions; j++) {\n+ switch(matrix_code) {\n+ case 1:\n+ simMat[i][j] = alternative_1_NTDegeneratedMatrix[i][j];\n+ break;\n+ }\n+ }\n+ }\n+\n+ /* Calculate the distances between residues based on Euclidean distance */\n+ for(j = 0; j < numPositions; j++) {\n+ for(i = 0; i < numPositions; i++) {\n+ if((i != j) && (distMat[i][j] == 0.0)) {\n+ for(k = 0, sum = 0; k < numPositions; k++)\n+ sum += ((simMat[k][j] - simMat[k][i]) * (simMat[k][j] - simMat[k][i]));\n+ sum = (float) sqrt(sum);\n+ distMat[i][j] = sum;\n+ distMat[j][i] = sum;\n+ }\n+ }\n+ }\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void similarityMatrix::printMatrix() |\n+| This method prints the similarity matrix to the standard output |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void similarityMatrix::printMatrix(){\n+\n+ for(int i = 0; i < numPositions; i++){\n+ for(int j = 0; j < numPositions; j++)\n+ cerr << setw(8) << setprecision(4) << right << simMat[i][j];\n+ cerr << endl;\n+ }\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| float similarityMatrix::getDistance(char,char) |\n+| This method returns the distance between the two characters given |\n+| The two character can be aminoacid characters, nucleotide characters |\n+| or any kind of characters. This depends on the defined characters in |\n+| the similarity matrix file. |\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+float similarityMatrix::getDistance(char a, char b){\n+ int numa, numb; char chA, chB;\n+\n+ chA = (char)toupper((int) a);\n+ chB = (char)toupper((int) b);\n+\n+ /* Search the first character position */\n+ if((chA >= \'A\') && (chA <= \'Z\')) numa = vhash[chA - \'A\'];\n+ else { cerr << "Error: the symbol \'" << a << "\' is incorrect" << endl; return -1; }\n+\n+ /* Search the second character position */\n+ if((chB >= \'A\') && (chB <= \'Z\')) numb = vhash[chB - \'A\'];\n+ else { cerr << "Error: the symbol \'" << b << "\' is incorrect" << endl; return -1; }\n+\n+ /* We check if the two character postions are valid positions */\n+ if(numa == -1) {\n+ cerr << "Error: the symbol \'" << a << "\' accesing the matrix is not defined in this object" << endl;\n+ return -1;\n+ }\n+\n+ if(numb == -1) {\n+ cerr << "Error: the symbol \'" << b << "\' accesing the matrix is not defined in this object" << endl;\n+ return -1;\n+ }\n+\n+ /* Return the distance value between a and b */\n+ return distMat[numa][numb];\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/similarityMatrix.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/similarityMatrix.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,70 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef SIMILARITYMATRIX_H
+#define SIMILARITYMATRIX_H
+
+#include <math.h>
+#include <ctype.h>
+#include <stdlib.h>
+
+#include <string>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+
+#include "defines.h"
+
+class similarityMatrix{
+ int *vhash;
+ float **simMat;
+ float **distMat;
+ int numPositions;
+
+ private:
+ void memoryAllocation(int);
+ void memoryDeletion();
+
+ public:
+ similarityMatrix();
+
+ ~similarityMatrix();
+
+ bool loadSimMatrix(char *);
+
+ void defaultAASimMatrix();
+
+ void defaultNTSimMatrix();
+
+ void defaultNTDegeneratedSimMatrix();
+
+ void alternativeSimilarityMatrices(int, int);
+
+ float getDistance(char, char);
+
+ void printMatrix();
+};
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statAl.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statAl.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,574 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ statAl v1.4: a tool for getting descriptive alignment features/scores.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of statAl.\n+\n+ statAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ statAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include <fstream>\n+#include <iostream>\n+#include <iomanip>\n+\n+#include <stdlib.h>\n+#include <string.h>\n+\n+#include "compareFiles.h"\n+#include "compareFiles.h"\n+#include "alignment.h"\n+#include "defines.h"\n+#include "utils.h"\n+\n+void show_menu(void);\n+void show_examples(void);\n+\n+int main(int argc, char *argv[]){\n+\n+ /* Input values */\n+ char *inFile = NULL, *forceFile = NULL, *setAlignments = NULL, *matrix = NULL;\n+ int windowSize = -1, gapWindow = -1, simWindow = -1, conWindow = -1,\n+ alternative_matrix = -1;\n+ bool stats_gaps_columns = 0, stats_gaps_dist = 0, stats_simil_columns = 0,\n+ stats_simil_dist = 0, stats_seqs_ident = 0, stats_col_ident_gen = 0,\n+ stats_file_columns = 0, stats_file_dist = 0;\n+ alignment *origAlig = NULL, **compAlig = NULL;\n+\n+ /* Internal variables */\n+ int i = 1, numFiles = 0, maxResidues = 0, referFile = 0, alignDataType = -1;\n+ similarityMatrix *similMatrix = NULL;\n+ char **filesToCompare = NULL;\n+ bool appearErrors = false;\n+ float *compareVect = NULL;\n+ ifstream algsPaths;\n+ string line;\n+\n+ /* ***** ***** ***** ***** ***** Help functions ***** ***** ***** ***** *** */\n+ /* Show help and exit either help flag is set or not arguments are provided */\n+ if((argc == 1) || ((!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) &&\n+ (i+1 == argc))) {\n+ show_menu();\n+ show_examples();\n+ return 0;\n+ }\n+\n+ /* Show version and revision if it is asked for */\n+ if((!strcmp(argv[i], "-v") || !strcmp(argv[i], "--version")) &&\n+ (i+1 == argc)) {\n+ cout << endl << "statAl v" << VERSION << ".rev" << REVISION\n+ << " build[" << BUILD << "]" << endl << endl;\n+ return 0;\n+ }\n+\n+ /* Allocate local memory for input alignment */\n+ origAlig = new alignment;\n+\n+ /* ***** ***** ***** ***** Input parameters loop ***** ***** ***** ***** ** */\n+ while(i < argc) {\n+\n+ /* Get input alignment */\n+ if((!strcmp(argv[i], "-i") || !strcmp(argv[i], "-in")) && (i+1 != argc) &&\n+ (inFile == NULL)) {\n+\n+ /* Try to load input alignment */\n+ inFile = new char[(int) strlen(argv[++i]) + 1];\n+ strcpy(inFile, argv[i]);\n+\n+ if(!origAlig -> loadAlignment(inFile)) {\n+ cerr << endl << "ERROR: Alignment not loaded: \\"" << inFile\n+ << "\\" Check input aligmment content." << endl << endl;\n+ appearErrors = true;\n+ }\n+ }\n+\n+ /* Force selection of a specific input alignment as a reference to perform\n+ * alignment comparisons */\n+ else if(!strcmp(argv[i], "-forceselect") && (i+1 != argc) &&\n+ (forceFile == NULL)) {\n+\n+ forceFile = new char[(int) strlen(argv[++i]) + 1];\n+ strcpy(forceFile, argv[i]);\n+\n+ if(!origAlig -> loadAlignment(forceFile)) {\n+ cerr << endl << "ERROR: Alignment not loaded: \\"" << forceFile\n+ << "\\" Check input aligmment content.'..b'nder the terms of the GNU General Public License as published by "\n+ << "the\\nFree Software Foundation, the last available version.\\n\\n";\n+\n+ cout << "Please cite:" << endl\n+ << "\\ttrimAl: a tool for automated alignment trimming in large-scale "\n+ << "phylogenetic analyses.\\n\\tSalvador Capella-Gutierrez; Jose M. Silla-"\n+ << "Martinez; Toni Gabaldon. Bioinformatics 2009, 25:1972-1973.\\n\\n";\n+\n+ cout << "Basic usage:" << endl\n+ << "\\tstatal -in <inputfile> (options)." << endl << endl;\n+\n+ cout << "Available options:" << endl << endl;\n+ cout << " -h --help "\n+ << "Print this information and show some examples." << endl;\n+ cout << " -v --version "\n+ << "Print the trimAl version." << endl << endl;\n+\n+ cout << " -i -in <inputfile> "\n+ << "Input file in several formats (clustal, fasta, nexus, phylip, etc)."\n+ << endl << endl;\n+\n+ cout << " -compareset <inputfile> "\n+ << "Input list of paths for the alignments to compare." << endl;\n+ cout << " -forceselect <inputfile> "\n+ << "Force selection of a given file as reference for being compare with "\n+ << "others." << endl << endl;\n+\n+ cout << " -matrix <inpufile> "\n+ << "Input file for user-defined similarity matrix (default: Blosum62)."\n+ << endl;\n+\n+ cout << " --alternative_matrix <name> "\n+ << "Select an alternative similarity matrix already loaded. " << endl\n+ << " "\n+ << "Only available \'degenerated_nt_identity\'" << endl << endl;\n+\n+ cout << " -sgc "\n+ << "Print gap score per column from input alignment." << endl;\n+ cout << " -sgt "\n+ << "Print accumulated gap scores distribution from input alignment."\n+ << endl << endl;\n+\n+ cout << " -ssc "\n+ << "Print similarity score per column from input alignment." << endl;\n+ cout << " -sst "\n+ << "Print accumulated similarity scores distribution for input alignment."\n+ << endl << endl;\n+\n+ cout << " -sfc "\n+ << "Print sum-of-pairs score per column for the selected alignment" << endl;\n+ cout << " -sft "\n+ << "Print accumulated sum-of-pairs scores distribution for the selected "\n+ << "alignment" << endl << endl;\n+\n+ cout << " -sident "\n+ << "Print identity scores for sequences in the alignemnt." << endl;\n+ cout << " -scolidentt "\n+ << "Print general descriptive statistics for column identity scores from "\n+ << "input alignemnt." << endl << endl;\n+\n+ cout << " -w <n> "\n+ << "(half) Window size, score of position i is the average of the window "\n+ << "(i - n) to (i + n)." << endl;\n+ cout << " -gw <n> "\n+ << "(half) Window size only applies to statistics based on Gaps." << endl;\n+ cout << " -sw <n> "\n+ << "(half) Window size only applies to statistics based on Similarity.\\n";\n+ cout << " -cw <n> "\n+ << "(half) Window size only applies to statistics based on Consistency."\n+ << endl << endl;\n+}\n+\n+void show_examples(void) {\n+\n+ cout << "Some Examples:" << endl << endl;\n+\n+ cout << "1) Get information about gaps distribution for input alignment"\n+ << endl << " statal -in <inputfile> -sgt" << endl << endl;\n+\n+ cout << "2) Get information about consistency score per column for the most "\n+ << "consistent input alignment, if more than one is provided"\n+ << endl << " statal -in <inputfile> -sfc" << endl << endl;\n+\n+ cout << "3) Get general descriptive statistics for columns identity"\n+ << endl << " statal -in <inputfile> -scolidentt" << endl << endl;\n+\n+ cout << "4) Change the windows size for computing similarity score per column"\n+ << endl << " statal -in <inputfile> -sw 3 -ssc" << endl << endl;\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statisticsConservation.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statisticsConservation.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,428 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl.\n+\n+ trimAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include "statisticsConservation.h"\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| statisticsConservation::statisticsConservation(char **, int, int) |\n+| |\n+| Class constructor. This method uses the inputs parameters to put the information in the new object that |\n+| has been created. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+statisticsConservation::statisticsConservation(string *alignmentMatrix, int species, int aminos, int dataType_) {\n+\n+ /* Initializate values to its corresponds values */\n+ columns = aminos;\n+ sequences = species;\n+ dataType = dataType_;\n+ halfWindow = -1;\n+\n+ /* Allocate memory to the structures and initializates it */\n+ Q = new float[columns];\n+ utils::initlVect(Q, columns, 0);\n+\n+ MDK = new float[columns];\n+ utils::initlVect(MDK, columns, 0);\n+\n+ MDK_Window = new float[columns];\n+ utils::initlVect(MDK_Window, columns, 0);\n+\n+ matrixIdentity = new float*[sequences];\n+ for(int i = 0; i < sequences; i++){\n+ matrixIdentity[i] = new float[sequences];\n+ utils::initlVect(matrixIdentity[i], sequences, 0);\n+ }\n+\n+ /* Initializate the similarity matrix to NULL. */\n+ simMatrix = NULL;\n+\n+ /* Calculation methods call */\n+ calculateMatrixIdentity(alignmentMatrix);\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| statisticsConservation::statisticsConservation(void) |\n+| |\n+| Class constructor. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+statisticsConservation::statisticsConservation(void) {\n+\n+ /* Initializate all values to 0 */\n+ columns = 0;\n+ sequences = 0;\n+ halfWindow = 0;\n+\n+ /* and the pointers to NULL */\n+ Q = NULL;\n+ MDK = NULL;\n+ MDK_Window = NULL;\n+\n+ matrixIdentity = NULL;\n+ simMatrix ='..b' cuttingPoint_SimilThreshold);\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void statisticsConservation::printConservationColumns(void) |\n+| |\n+| This method prints the conservation\'s value for each column in the alignment. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void statisticsConservation::printConservationColumns(void) {\n+\n+ int i;\n+\n+ /* We set the output precision and print the header. */\n+ cout << "| Residue\\t Similarity |" << endl;\n+ cout << "| Number \\t Value |" << endl;\n+ cout << "+----------------------------+" << endl;\n+ cout.precision(10);\n+\n+ /* If MDK_Window vector is defined, we use it to print the conservation\'s values. */\n+ if(MDK_Window != NULL)\n+ for(i = 0; i < columns; i++)\n+ cout << " " << setw(5) << i << "\\t\\t" << setw(7) << MDK_Window[i] << endl;\n+\n+ /* In others cases, we uses the MDK vector to print the conservation\'s vlaues. */\n+ else\n+ for(i = 0; i < columns; i++)\n+ cout << " " << setw(5) << i << "\\t\\t" << setw(7) << MDK[i] << endl;\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void statisticsConservation::printConservationAcl(void) |\n+| |\n+| This method prints the accumulative statistics related to conservation in the alignment. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void statisticsConservation::printConservationAcl(void) {\n+\n+ float refer, *vectAux;\n+ int i, num, acm;\n+\n+ /* Allocate memory */\n+ vectAux = new float[columns];\n+\n+ /* Select the conservation\'s value source and copy that vector in a auxiliar vector */\n+ if(MDK_Window != NULL) utils::copyVect(MDK_Window, vectAux, columns);\n+ else utils::copyVect(MDK, vectAux, columns);\n+\n+ /* Sort the auxiliar vector. */\n+ utils::quicksort(vectAux, 0, columns-1);\n+\n+ /* We set the output precision and print the header. */\n+ cout << "| Number of\\t \\t|\\t Cumulative \\t% Cumulative\\t| Similarity |" << endl;\n+ cout << "| Residues \\t% Length\\t|\\tNumberResid.\\t Length \\t| Value |" << endl;\n+ cout << "+-------------------------------+---------------------------------------+----------------+" << endl;\n+ cout.precision(10);\n+\n+\n+ /* Initializate some values */\n+ refer = vectAux[columns-1];\n+ acm = 0; num = 1;\n+\n+ /* Count the columns with the same conservation\'s value and compute this information to shows the accunulative\n+ statistics in the alignment. */\n+ for(i = columns-2; i >= 0; i--) {\n+ acm++;\n+\n+ if(refer != vectAux[i]) {\n+ cout << " " << num << "\\t\\t" << setw(10) << ((float) num/columns * 100.0)\n+ << "\\t\\t" << acm << "\\t\\t" << setw(10) << ((float) acm/columns * 100.0) << "\\t"\n+ << setw(15) << refer << endl;\n+ refer = vectAux[i];\n+ num = 1;\n+ }\n+ else num++;\n+ }\n+ acm++;\n+ cout << " " << num << "\\t\\t" << setw(10) << ((float) num/columns * 100.0)\n+ << "\\t\\t" << acm << "\\t\\t" << setw(10) << ((float) acm/columns * 100.0) << "\\t"\n+ << setw(15) << refer << endl;\n+\n+ /* Deallocate the reserved memory. */\n+ delete [] vectAux;\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statisticsConservation.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statisticsConservation.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,112 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef STATISTICS_CONSERVATION_H
+#define STATISTICS_CONSERVATION_H
+
+#include <math.h>
+#include <iostream>
+#include <iomanip>
+
+#include "similarityMatrix.h"
+#include "statisticsGaps.h"
+#include "defines.h"
+#include "utils.h"
+
+using namespace std;
+
+/* ***************************************************************************************************************** */
+/* Header Class File: StatisticsConservation. */
+/* ***************************************************************************************************************** */
+
+class statisticsConservation{
+ private:
+
+ /* Number of columns and sequences of the alignment */
+ int columns;
+ int sequences;
+
+ /* Sequence's Datatype: DNA, RNA or Amino Acids. */
+ int dataType;
+
+ /* Half window size */
+ int halfWindow;
+
+ /* Conservation vectors */
+ float *Q;
+ float *MDK;
+ float *MDK_Window;
+
+ /* Identity weight matrix between alignment rows */
+ float **matrixIdentity;
+
+ /* Similarity matrix used to conservation calculations */
+ similarityMatrix *simMatrix;
+
+ /* Private methods */
+ /* Computes the matrix identity between alignment's columns. */
+ void calculateMatrixIdentity(string *alignmentMatrix);
+
+ public:
+
+ /* Constructors without any parameters */
+ statisticsConservation(void);
+
+ /* Constructors using parameters */
+ statisticsConservation(string *, int, int, int);
+
+ /* Destroyer */
+ ~statisticsConservation(void);
+
+ /* This methods allows us compute the alignment's conservation's values. */
+ bool calculateVectors(string *, int *);
+
+ /* Allows us compute the conservationWindow's values. */
+ bool applyWindow(int);
+
+ /* Returns if a windows size value has been defined or not. */
+ bool isDefinedWindow(void);
+
+ /* This methods returns a pointer to conservationWindow's vector */
+ float *getMdkwVector(void);
+
+ /* Associates a pointer to similarity matrix. This matrix is needed to compute the conservation's values. */
+ bool setSimilarityMatrix(similarityMatrix *);
+
+ /* Returns if a similarity matrix is being used or not. */
+ bool isSimMatrixDef(void);
+
+ /* Computes and selects the cut point values based on conservation's values. */
+ double calcCutPoint(float, float);
+
+ /* Prints the conservation's value for each alignment's column. */
+ void printConservationColumns(void);
+
+ /* Computes and prints the accumulative statistics associated to the alignment. */
+ void printConservationAcl(void);
+
+};
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statisticsFiles.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statisticsFiles.cpp Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,56 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#include "statisticsFiles.h"
+
+statisticsFiles::statisticsFiles() {
+ columns = 0;
+ columnLength = 0;
+ sequencesMatrix = NULL;
+}
+
+statisticsFiles::statisticsFiles(char **alignmentMatrix, int species, int aminos) {
+ int i;
+
+ columnLength = species;
+ columns = aminos;
+
+ sequencesMatrix = new int*[columnLength];
+ for(i = 0; i < columnLength; i++)
+ sequencesMatrix[i] = new int[columns];
+}
+
+statisticsFiles::~statisticsFiles() {
+ int i;
+
+ for(i = 0; i < columnLength; i++)
+ delete[] sequencesMatrix[i];
+ delete[] sequencesMatrix;
+
+ sequencesMatrix = NULL;
+ columnLength = 0;
+ columns = 0;
+}

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statisticsFiles.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statisticsFiles.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,48 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef STATISTICSFILES_H
+#define STATISTICSFILES_H
+
+#include <iostream>
+#include <iomanip>
+
+#include "utils.h"
+
+class statisticsFiles {
+
+ int **sequencesMatrix;
+ int columns;
+ int columnLength;
+
+ public:
+ statisticsFiles();
+ statisticsFiles(char **alignmentMatrix, int species, int aminos);
+
+ ~statisticsFiles();
+};
+
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statisticsGaps.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statisticsGaps.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,464 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl.\n+\n+ trimAl is free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include "statisticsGaps.h"\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| statisticsGaps::statisticsGaps(char **, int, int) |\n+| |\n+| Class constructor. This method uses the inputs parameters to put the information in the new object that |\n+| has been created. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+statisticsGaps::statisticsGaps(string *alignmentMatrix, int species, int aminos, int dataType_) {\n+\n+ int i, j;\n+ char indet;\n+\n+ columnLength = species;\n+ columns = aminos;\n+ maxGaps = 0;\n+ halfWindow = 0;\n+ dataType = dataType_;\n+\n+ if(dataType == AAType)\n+ indet = \'X\';\n+ else\n+ indet = \'N\';\n+\n+ /* Memory allocation for the vectors and its initialization */\n+ gapsInColumn = new int[columns];\n+ utils::initlVect(gapsInColumn, columns, 0);\n+\n+ aminosXInColumn = new int[columns];\n+ utils::initlVect(aminosXInColumn, aminos, 0);\n+\n+ gapsWindow = new int[columns];\n+ utils::initlVect(gapsWindow, columns, 0);\n+\n+ numColumnsWithGaps = new int[species+1];\n+ utils::initlVect(numColumnsWithGaps, columnLength+1, 0);\n+\n+ /* Count the gaps and indeterminations of each columns */\n+ for(i = 0; i < columns; i++) {\n+ for(j = 0; j < columnLength; j++) {\n+ if(alignmentMatrix[j][i] == \'-\')\n+ gapsInColumn[i]++;\n+ else if(alignmentMatrix[j][i] == indet)\n+ aminosXInColumn[i]++;\n+ }\n+\n+ /* Increase the number of colums with the number of gaps of the last processed column */\n+ numColumnsWithGaps[gapsInColumn[i]]++;\n+ gapsWindow[i] = gapsInColumn[i];\n+ if(gapsWindow[i] > maxGaps) maxGaps = gapsWindow[i];\n+ }\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| statisticsGaps::statisticsGaps(void) |\n+| |\n+| Class constructor. |\n+| |\n+'..b'ev]);\n+ max = pprev;\n+ }\n+ }\n+ act = prev;\n+ }\n+\n+ /* We deallocate local memory. */\n+ delete[] secondSlopeVector;\n+\n+ /* Finally, we return the selected cut point. */\n+ return max;\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void statisticsGaps::printGapsColumns(void) |\n+| |\n+| This method shows the gaps\' percentage per each column in the alignment. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void statisticsGaps::printGapsColumns(void) {\n+\n+ int *vectAux;\n+\n+ /* We allocate a local vector to recovery information on it */\n+ vectAux = new int[columns];\n+\n+ /* We decide about the information\'s source then we get the information. */\n+ if(halfWindow == 0)\n+ utils::copyVect(gapsInColumn, vectAux, columns);\n+ else\n+ utils::copyVect(gapsWindow, vectAux, columns);\n+\n+ /* Fix the precision of output */\n+ /* We set the output precision and print the header. */\n+ cout << "| Residue\\t % Gaps \\t Gap Score |" << endl;\n+ cout << "| Number \\t \\t |" << endl;\n+ cout << "+----------------------------------------------+" << endl;\n+ cout.precision(10);\n+\n+ /* Show the information that have been requered */\n+ for(int i = 0; i < columns; i++)\n+ cout << " " << setw(5) << i << "\\t\\t" << setw(10) << (vectAux[i] * 100.0)/columnLength\n+ << "\\t" << setw(7) << 1 -((vectAux[i] * 1.0)/columnLength) << endl;\n+\n+ /* Finally, we deallocate the local memory */\n+ delete[] vectAux;\n+}\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+| void statisticsGaps::printGapsAcl(void) |\n+| |\n+| This method shows the gaps\' statistics for the alignment. |\n+| |\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void statisticsGaps::printGapsAcl(void) {\n+\n+ int acm, i;\n+\n+ /* Fix the precision of output */\n+ cout << "| Number of\\t \\t|\\t Cumulative \\t% Cumulative\\t|\\tNumber of Gaps\\t % Gaps \\tGap Score |" << endl;\n+ cout << "| Residues \\t% Length\\t|\\tNumberResid.\\t Length \\t|\\t per Column \\tper Column\\tper Column |" << endl;\n+ cout << "+-------------------------------+-----------------------------"\n+ << "----------+--------------------------------------------------+" << endl;\n+ cout.precision(10);\n+\n+ /* Count for each gaps\' number the columns\' number with that gaps\' number. */\n+ for(i = 0, acm = 0; i <= maxGaps; i++) {\n+\n+ /* If the columns\' number with this gaps\' number is not equal to zero, we will count the columns. */\n+ if(numColumnsWithGaps[i] != 0) {\n+\n+ /* Compute and prints the accumulative values for the gaps in the alignment. */\n+ acm += numColumnsWithGaps[i];\n+ cout << " " << setiosflags(ios::left) << numColumnsWithGaps[i] << "\\t\\t" << setw(10) << (numColumnsWithGaps[i] * 100.0)/columns\n+ << "\\t\\t" << acm << "\\t\\t" << setw(10) << (acm * 100.0)/columns\n+ << "\\t\\t" << i << "\\t\\t" << setw(10) << (i * 1.0)/columnLength << "\\t"<< setw(10) << 1 - ((i * 1.0)/columnLength) << endl;\n+ }\n+ }\n+}\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/statisticsGaps.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/statisticsGaps.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,87 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+#ifndef STATISTICSGAPS_H
+#define STATISTICSGAPS_H
+
+#include <iostream>
+#include <iomanip>
+
+#include "utils.h"
+#include "defines.h"
+
+using namespace std;
+
+/* ***************************************************************************************************************** */
+/* Header Class File: StatisticsGaps. */
+/* ***************************************************************************************************************** */
+
+class statisticsGaps {
+
+ int columns;
+ int columnLength;
+ int maxGaps;
+ int halfWindow;
+ int dataType;
+
+ int *gapsInColumn;
+ int *numColumnsWithGaps;
+ int *aminosXInColumn;
+ int *gapsWindow;
+
+ public:
+
+ /* Class constructor without parameters. */
+ statisticsGaps(void);
+
+ /* Class destroyer. */
+ ~statisticsGaps(void);
+
+ /* Class constructor with parameters. */
+ statisticsGaps(string *, int, int, int);
+
+ /* Methods allows us compute the gapWindows' values. */
+ bool applyWindow(int);
+
+ /* This methods returns a gaps' vector reference. */
+ int *getGapsWindow(void);
+
+ /* Allows compute and select the cut point value. */
+ double calcCutPoint(float, float);
+
+ /* Automatic method to find a cut point value using the first and the second slopes. */
+ int calcCutPointMixSlope(void);
+
+ /* Automatic method to compute a cut point valur using the second slope approach. */
+ int calcCutPoint2ndSlope(void);
+
+ /* This methods print the gaps' percentage of each column in the alignment. */
+ void printGapsColumns(void);
+
+ /* This methods prints the statistics for the alignment relates to gaps. */
+ void printGapsAcl(void);
+
+};
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/utils.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/utils.cpp Fri Mar 25 17:10:43 2022 +0000

[

b'@@ -0,0 +1,850 @@\n+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+\n+ trimAl v1.4: a tool for automated alignment trimming in large-scale\n+ phylogenetics analyses.\n+\n+ readAl v1.4: a tool for automated alignment conversion among different\n+ formats.\n+\n+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.\n+ [scapella, tgabaldon]@crg.es\n+\n+ This file is part of trimAl/readAl.\n+\n+ trimAl/readAl are free software: you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation, the last available version.\n+\n+ trimAl/readAl are distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.\n+\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****\n+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+#include "utils.h"\n+#include "values.h"\n+#include "defines.h"\n+\n+/*++++++++++++++++++++++++++++++++++++++++++++++++\n+| void utils::initVect(int *, int, int) |\n+| This method is used to initializate all |\n+| positions of a vector with a given value. |\n+++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void utils::initlVect(int *vector, int tam, int valor) {\n+\n+ for(int i = 0; i < tam; i++) vector[i] = valor;\n+\n+}\n+\n+void utils::initlVect(float *vector, int tam, float valor) {\n+\n+ for(int i = 0; i < tam; i++) vector[i] = valor;\n+\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++++++\n+| void utils::copyVect(int *, int *, int) |\n+| This method copies integer vector 1 to |\n+| integer vector 2. |\n++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void utils::copyVect(int *vect1, int *vect2, int tam) {\n+\n+ for(int i = 0; i < tam; i++) vect2[i] = vect1[i];\n+\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++++++++\n+| void utils::copyVect(float *, float *, float) |\n+| This method copies float vector 1 to |\n+| float vector 2. |\n++++++++++++++++++++++++++++++++++++++++++++++++*/\n+\n+void utils::copyVect(float *vect1, float *vect2, int tam) {\n+\n+ for(int i = 0; i < tam; i++) vect2[i] = vect1[i];\n+\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++\n+| int utils::roundToInf(double) |\n+| This method rounds a double number |\n+| to the inferior integer. |\n++++++++++++++++++++++++++++++++++++++++++*/\n+\n+int utils::roundToInf(double number) {\n+\n+ return ((int) number);\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++\n+| int utils::roundInt(double) |\n+| This method rounds a double number |\n+| to a integer. |\n++++++++++++++++++++++++++++++++++++++++++*/\n+\n+int utils::roundInt(double number) {\n+\n+ return ((int) ((double) number + 0.5));\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++\n+| int utils::roundToSup(double) |\n+| This method rounds a double number |\n+| to the greater integer. |\n++++++++++++++++++++++++++++++++++++++++++*/\n+\n+int utils::roundToSup(double number) {\n+\n+ return ((int) ((double) number + 1.0));\n+}\n+\n+\n+/*+++++++++++++++++++++++++++++++++++++++++\n+| int utils::max(int, int) |\n+| This method returns the maximum |\n+| value of the two given arguments. |\n++++++++++++++++++++++++++++++++++++++++++*/\n+\n+int utils::max(int x, int y) {\n+\n+ if(x > y) return x;\n+ else return y;\n+}\n+\n+float utils::max(float x, float y) {\n+\n+ if(x > y) return x;\n+ else return y;\n+}\n+\n+double '..b'\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (K, R): {60%, kr}{85%, q} */\n+ case 75: case 82:\n+ if(lookForPattern(column, "kr", 0.6)) return \'r\';\n+ else if(lookForPattern(column, "q", 0.85)) return \'r\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (T): {50%, ts}{60%, wlvimafcyhp } */\n+ case 84:\n+ if(lookForPattern(column, "ts", 0.5)) return \'g\';\n+ else if(lookForPattern(column, "wlvimafcyhp", 0.6)) return \'g\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (S): {50%, ts}{80%, wlvimafcyhp } */\n+ case 83:\n+ if(lookForPattern(column, "ts", 0.5)) return \'g\';\n+ else if(lookForPattern(column, "wlvimafcyhp", 0.8)) return \'g\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (N): {50%, n}{85%, d } */\n+ case 78:\n+ if(lookForPattern(column, "n", 0.5)) return \'g\';\n+ else if(lookForPattern(column, "d", 0.85)) return \'g\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (Q): {50%, qe}{60%, kr} */\n+ case 81:\n+ if(lookForPattern(column, "qe", 0.5)) return \'g\';\n+ else if(lookForPattern(column, "kr", 0.6)) return \'g\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (D): {50%, de, n} */\n+ case 68:\n+ if(lookForPattern(column, "de", 0.5)) return \'m\';\n+ else if(lookForPattern(column, "n", 0.5)) return \'m\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (E): {50%, de,qe} */\n+ case 69:\n+ if(lookForPattern(column, "de", 0.5)) return \'m\';\n+ else if(lookForPattern(column, "qe", 0.5)) return \'m\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ /* (H,Y): {50%, p}{60%, wlvimafcyhp} */\n+ case 72: case 89:\n+ if(lookForPattern(column, "p", 0.5)) return \'c\';\n+ else if(lookForPattern(column, "wlvimafcyhp", 0.5)) return \'c\';\n+ else return \'w\';\n+ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */\n+ }\n+ }\n+ return \'w\';\n+}\n+\n+\n+bool utils::lookForPattern(string column, string dataset, float level) {\n+\n+ float count = 0;\n+ int i, j;\n+\n+ for(i = 0; i < (int) column.size(); i++) {\n+ for(j = 0; j < (int) dataset.size(); j++) {\n+ if(toupper(column[i]) == toupper(dataset[j])) {\n+ count++; break;\n+ }\n+ }\n+ }\n+\n+ if((count/column.size()) >= level)\n+ return true;\n+ else return false;\n+}\n+\n'

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/utils.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/utils.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,207 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ readAl v1.4: a tool for automated alignment conversion among different
+ formats.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl/readAl.
+
+ trimAl/readAl are free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl/readAl are distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef UTILS_H
+#define UTILS_H
+
+#include <string.h>
+#include <stdlib.h>
+
+#include <fstream>
+#include <iostream>
+
+/** \brief Utils class.
+ *
+ * This class implements util methods.
+ */
+
+using namespace std;
+
+class utils {
+
+ public:
+ /** \brief Vector initialization.
+ * \param vector The vector that will be initializated.
+ * \param tam The size of the vector.
+ * \param valor The initialization value of all positions of the vector.
+ *
+ * This method is used to initializate all positions of a vector with a given value.
+ */
+ static void initlVect(int *vector, int tam, int valor);
+ static void initlVect(float *vector, int tam, float valor);
+
+ /** \brief Integer vector copying.
+ * \param vect1 Vector that we want to copy.
+ * \param vect2 Destination vector of the copy.
+ * \param tam Vectors size.
+ *
+ * This method copies integer vector 1 to integer vector 2.
+ */
+ static void copyVect(int *vect1, int *vect2, int tam);
+
+ /** \brief Float vector copying.
+ * \param vect1 Vector that we want to copy.
+ * \param vect2 Destination vector of the copy.
+ * \param tam Vectors size.
+ *
+ * This method copies float vector 1 to float vector 2.
+ */
+ static void copyVect(float *vect1, float *vect2, int tam);
+
+ /** \brief Round double to inferior integer method.
+ * \param number The number that will be rounded.
+ * \return the rounded number.
+ *
+ * This method rounds a double number to the inferior integer.
+ */
+ static int roundToInf(double number);
+
+ /** \brief Round double to integer method.
+ * \param number The number that will be rounded.
+ * \return the rounded number.
+ *
+ * This method rounds a double number to a integer.
+ */
+ static int roundInt(double number);
+
+ /** \brief Round double to greater integer method.
+ * \param number The number that will be rounded.
+ * \return the rounded number.
+ *
+ * This method rounds a double number to the greater integer.
+ */
+ static int roundToSup(double number);
+
+ /** \brief Maximum of two numbers method.
+ * \param x The first number.
+ * \param y The second number.
+ * \return The maximum between the two given numbers.
+ *
+ * This method returns the maximum between the two numbers given as parameters.
+ */
+ static int max(int x, int y);
+
+ static float max(float x, float y);
+
+ static double max(double x, double y);
+
+ static int min(int x, int y);
+
+ static float min(float x, float y);
+
+ static double min(double x, double y);
+
+ // static bool getArg(int argc, char *argv[], int *var, char *argument, char *abrevArg);
+ /** \brief String-is-number checking.
+ * \param num The string we want to check.
+ * \return \b true if the string is a number, \b false if not.
+ *
+ * This method checks if the given string is a float number.
+ */
+ static bool isNumber(char *num);
+
+ /** \brief String comparing method.
+ * \param a The first string that will be compared.
+ * \param b The second string that will be compared.
+ * \return \b true if the two strings are the same, \b false if not.
+ *
+ * This method compares the two strings given, and returns \b true if the two strings are equal.
+ */
+ static bool compare(char *a, char *b);
+
+ /** \brief Removing spaces method.
+ * \param in The string that we want to clean.
+ * \param out The destination of the clean string.
+ *
+ * This method removes spaces in the input string and put the result in the output string.
+ */
+ static void removeSpaces(char *in, char *out);
+
+ /** \brief Quicksort sorting method.
+ * \a param list The vector that we want to sort.
+ * \a param ini The first element of the vector.
+ * \a param fin The last element of the vector.
+ *
+ * This method sorts the vector using the quicksort method.
+ */
+ static void quicksort(float *list, int ini, int fin);
+
+ /** \brief Swapping elements method
+ * \param a One element to swap.
+ * \param b Other element to swap.
+ *
+ * This method swaps the values in a and b.
+ */
+ static void swap(float *a, float *b);
+
+ /** \brief Quicksort sorting method.
+ * \a param list The vector that we want to sort.
+ * \a param ini The first element of the vector.
+ * \a param fin The last element of the vector.
+ *
+ * This method sorts the vector using the quicksort method.
+ */
+ static void quicksort(int *list, int ini, int fin);
+
+ /** \brief Swapping elements method
+ * \param a One element to swap.
+ * \param b Other element to swap.
+ *
+ * This method swaps the values in a and b.
+ */
+ static void swap(int *a, int *b);
+
+ static bool checkFile(ifstream &file);
+
+ static char* readLine(ifstream &file);
+
+ static char* trimLine(string nline);
+
+ static char* readLineMEGA(ifstream &file);
+
+ static string getReverse(string toReverse);
+
+ static string removeCharacter(char c, string line);
+
+ static int checkTypeAlignment(int, int, string *);
+
+ static int* readNumbers(string);
+
+ static int* readNumbers_StartEnd(string);
+
+ static void quicksort(int **, int, int);
+
+ static void swap(int **, int **);
+
+ static char determineColor(char res, string column);
+
+ static bool lookForPattern(string, string, float);
+
+};
+#endif

diff -r 000000000000 -r b15a3147e604 trimal_repo/source/values.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/values.h Fri Mar 25 17:10:43 2022 +0000

[

@@ -0,0 +1,119 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+ ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+ trimAl v1.4: a tool for automated alignment trimming in large-scale
+ phylogenetics analyses.
+
+ 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+ [scapella, tgabaldon]@crg.es
+
+ This file is part of trimAl.
+
+ trimAl is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, the last available version.
+
+ trimAl is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with trimAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifdef SIMMatrix
+
+/* Characters used for different alignments type */
+char listNTSym[6] = "ACGTU";
+
+char listAASym[21] = "ARNDCQEGHILKMFPSTWYV";
+
+char listNTDegenerateSym[16] = "ACGTURYKMSWBDHV";
+
+/* Characters used to indicate indeterminations */
+char protein_wildcards[3] = "BX";
+
+/* Pyrrolysine: 'O' > 'TAG' */
+/* Selenocysteine: 'U' > 'TGA' */
+char protein_alternative_aminoacids[3] = "UO";
+
+/* Default Identity Matrix for Canonical Nucleotides */
+float defaultNTMatrix[5][5] = {
+ {1, 0, 0, 0, 0},
+ {0, 1, 0, 0, 0},
+ {0, 0, 1, 0, 0},
+ {0, 0, 0, 1, 0},
+ {0, 0, 0, 0, 1}
+};
+
+float defaultNTDegeneratedMatrix[15][15] = {
+/* A: adenosine (A) C: cytidine (C) G: guanine (G) T: thymidine (T) U: uridine (U)
+ * R: purine (G | A) Y: pyrimidine (C | T/u) K: keto (G | T/u) M: amino (A | C) S: strong (G | C)
+ * W: weak (A | T/u) B: not A (G | C | T/u) D: not C (G | A | T/u) H: not G (A | C | T/u) V: not T/u (G | C | A) */
+ { 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 1/4., 0.0, 1/4., 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 1/4., 0.0, 1/4., 1/4., 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 0.0, 1/4., 1/4., 1/4., 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 1/4., 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 1/4., 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0},
+ { 1/4., 0.0, 0.0, 1/4., 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0},
+ { 0.0, 1/6., 1/6., 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6., 0.0, 0.0, 0.0},
+ { 1/6., 0.0, 1/6., 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6., 0.0, 0.0},
+ { 1/6., 1/6., 0.0, 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6., 0.0},
+ { 1/6., 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6.}
+};
+
+/* BLOSUM62 Similarity Matrix */
+float defaultAAMatrix[20][20] = {
+ { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0},
+ { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3},
+ { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3},
+ { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3},
+ { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1},
+ { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2},
+ { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2},
+ { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3},
+ { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3},
+ { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3},
+ { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1},
+ { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2},
+ { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1},
+ { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1},
+ { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2},
+ { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2},
+ { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0},
+ { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3},
+ { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1},
+ { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}
+};
+
+
+/* Alternative matrixes */
+
+// Nucleotides
+float alternative_1_NTDegeneratedMatrix[15][15] = {
+ { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0},
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1}
+};
+
+#endif