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Changeset 1:98944ec4bfc7 (2022-03-25)

Previous changeset 0:b15a3147e604 (2022-03-25) Next changeset 2:0d53577b962f (2022-04-11)

Commit message:
Deleted selected files

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/AUTHORS
--- a/trimal_repo/AUTHORS Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-** 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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/CHANGELOG
--- a/trimal_repo/CHANGELOG Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,150 +0,0 @@
-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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/LICENSE
--- a/trimal_repo/LICENSE Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,674 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/README
--- a/trimal_repo/README Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/alignments_comparison.1
--- a/trimal_repo/dataset/alignments_comparison.1 Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/alignments_comparison.2
--- a/trimal_repo/dataset/alignments_comparison.2 Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/alignments_comparison.3
--- a/trimal_repo/dataset/alignments_comparison.3 Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.001.AA.clw
--- a/trimal_repo/dataset/example.001.AA.clw Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,10 +0,0 @@
-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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.001.AA.msl
--- a/trimal_repo/dataset/example.001.AA.msl Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,9 +0,0 @@
- 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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.001.AA.phy
--- a/trimal_repo/dataset/example.001.AA.phy Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,9 +0,0 @@
- 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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.002.AA.clw
--- a/trimal_repo/dataset/example.002.AA.clw Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.002.AA.phy
--- a/trimal_repo/dataset/example.002.AA.phy Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
- 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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.003.AA.clw
--- a/trimal_repo/dataset/example.003.AA.clw Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.004.AA.fasta
--- a/trimal_repo/dataset/example.004.AA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.005.AA.fasta
--- a/trimal_repo/dataset/example.005.AA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.006.AA.pir
--- a/trimal_repo/dataset/example.006.AA.pir Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,62 +0,0 @@
->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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.007.AA.fasta
--- a/trimal_repo/dataset/example.007.AA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,528 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.007.AA.only_seqs
--- a/trimal_repo/dataset/example.007.AA.only_seqs Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,286 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.009.AA.fasta
--- a/trimal_repo/dataset/example.009.AA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,45 +0,0 @@
->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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.010.AA.fasta
--- a/trimal_repo/dataset/example.010.AA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.011.AA.YKL197C.clw
--- a/trimal_repo/dataset/example.011.AA.YKL197C.clw Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,852 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.011.AA.YKL197C.fasta
--- a/trimal_repo/dataset/example.011.AA.YKL197C.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,747 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.011.AA.YKL197C.phy
--- a/trimal_repo/dataset/example.011.AA.YKL197C.phy Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,674 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.012.AA.SuperAlignment.phy
--- a/trimal_repo/dataset/example.012.AA.SuperAlignment.phy Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,38803 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.013.AA.SuperAlignment.phy
--- a/trimal_repo/dataset/example.013.AA.SuperAlignment.phy Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,21346 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.014.AA.EggNOG.COG0591.fasta
--- a/trimal_repo/dataset/example.014.AA.EggNOG.COG0591.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,440709 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta
--- a/trimal_repo/dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,239148 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta
--- a/trimal_repo/dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,5852 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta
--- a/trimal_repo/dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2842 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta
--- a/trimal_repo/dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4266 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta
--- a/trimal_repo/dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,7665 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta
--- a/trimal_repo/dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,9030 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta
--- a/trimal_repo/dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2373 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta
--- a/trimal_repo/dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3184 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta
--- a/trimal_repo/dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,55188 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta
--- a/trimal_repo/dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,354 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta
--- a/trimal_repo/dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,31844 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta
--- a/trimal_repo/dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,11320 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta
--- a/trimal_repo/dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1071 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta
--- a/trimal_repo/dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,11900 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta
--- a/trimal_repo/dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2985 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta
--- a/trimal_repo/dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3978 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta
--- a/trimal_repo/dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4305 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta
--- a/trimal_repo/dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,7831 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta
--- a/trimal_repo/dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,9792 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta
--- a/trimal_repo/dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,32054 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta
--- a/trimal_repo/dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,12238 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta
--- a/trimal_repo/dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2600 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta
--- a/trimal_repo/dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4656 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta
--- a/trimal_repo/dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,5275 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta
--- a/trimal_repo/dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,73612 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta
--- a/trimal_repo/dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,10286 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta
--- a/trimal_repo/dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1246 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta
--- a/trimal_repo/dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1888 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta
--- a/trimal_repo/dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,756 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta
--- a/trimal_repo/dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1694 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta
--- a/trimal_repo/dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,492 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta
--- a/trimal_repo/dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,480 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta
--- a/trimal_repo/dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,480 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
--- a/trimal_repo/dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,350 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta
--- a/trimal_repo/dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,462 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
--- a/trimal_repo/dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,372 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
--- a/trimal_repo/dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,720 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta
--- a/trimal_repo/dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,790 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta
--- a/trimal_repo/dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,256 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta
--- a/trimal_repo/dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,636 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta
--- a/trimal_repo/dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,155 +0,0 @@
->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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
--- a/trimal_repo/dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,340 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
--- a/trimal_repo/dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1212 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.058.AA.strNOG.ENOG411BBR6.fasta
--- a/trimal_repo/dataset/example.058.AA.strNOG.ENOG411BBR6.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,341 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.059.AA.strNOG.ENOG411BBRR.fasta
--- a/trimal_repo/dataset/example.059.AA.strNOG.ENOG411BBRR.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,378 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.060.AA.strNOG.ENOG411BBWK.fasta
--- a/trimal_repo/dataset/example.060.AA.strNOG.ENOG411BBWK.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1190 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta
--- a/trimal_repo/dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1023 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.062.AA.strNOG.ENOG411BCX3.fasta
--- a/trimal_repo/dataset/example.062.AA.strNOG.ENOG411BCX3.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,22869 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.063.AA.strNOG.ENOG411BDBU.fasta
--- a/trimal_repo/dataset/example.063.AA.strNOG.ENOG411BDBU.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,420 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.064.AA.strNOG.ENOG411BDKC.fasta
--- a/trimal_repo/dataset/example.064.AA.strNOG.ENOG411BDKC.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4914 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta
--- a/trimal_repo/dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,960 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.066.AA.strNOG.ENOG411BDUE.fasta
--- a/trimal_repo/dataset/example.066.AA.strNOG.ENOG411BDUE.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,560 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.067.AA.strNOG.ENOG411BDX3.fasta
--- a/trimal_repo/dataset/example.067.AA.strNOG.ENOG411BDX3.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1050 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.068.AA.strNOG.ENOG411BE45.fasta
--- a/trimal_repo/dataset/example.068.AA.strNOG.ENOG411BE45.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,360 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.069.AA.strNOG.ENOG411BE8B.fasta
--- a/trimal_repo/dataset/example.069.AA.strNOG.ENOG411BE8B.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,470 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.070.AA.strNOG.ENOG411BEUV.fasta
--- a/trimal_repo/dataset/example.070.AA.strNOG.ENOG411BEUV.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1254 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta
--- a/trimal_repo/dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1125 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.072.AA.strNOG.ENOG411BF1S.fasta
--- a/trimal_repo/dataset/example.072.AA.strNOG.ENOG411BF1S.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,279 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.073.AA.strNOG.ENOG411BFCW.fasta
--- a/trimal_repo/dataset/example.073.AA.strNOG.ENOG411BFCW.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,49005 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.074.AA.strNOG.ENOG411BFPF.fasta
--- a/trimal_repo/dataset/example.074.AA.strNOG.ENOG411BFPF.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,527 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.075.AA.strNOG.ENOG411BFQS.fasta
--- a/trimal_repo/dataset/example.075.AA.strNOG.ENOG411BFQS.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,420 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.076.AA.strNOG.ENOG411BH75.fasta
--- a/trimal_repo/dataset/example.076.AA.strNOG.ENOG411BH75.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,697 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.077.AA.strNOG.ENOG411BH79.fasta
--- a/trimal_repo/dataset/example.077.AA.strNOG.ENOG411BH79.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1450 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.078.AA.strNOG.ENOG411BH99.fasta
--- a/trimal_repo/dataset/example.078.AA.strNOG.ENOG411BH99.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,903 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.079.AA.strNOG.ENOG411BJDC.fasta
--- a/trimal_repo/dataset/example.079.AA.strNOG.ENOG411BJDC.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,310 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.080.AA.strNOG.ENOG411BJIF.fasta
--- a/trimal_repo/dataset/example.080.AA.strNOG.ENOG411BJIF.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,496 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.081.AA.strNOG.ENOG411BK9X.fasta
--- a/trimal_repo/dataset/example.081.AA.strNOG.ENOG411BK9X.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,287 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.082.AA.strNOG.ENOG411BKC5.fasta
--- a/trimal_repo/dataset/example.082.AA.strNOG.ENOG411BKC5.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,546 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.083.AA.strNOG.ENOG411BMKC.fasta
--- a/trimal_repo/dataset/example.083.AA.strNOG.ENOG411BMKC.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,297 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.084.AA.strNOG.ENOG411BNP9.fasta
--- a/trimal_repo/dataset/example.084.AA.strNOG.ENOG411BNP9.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,231 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta
--- a/trimal_repo/dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,248 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.086.AA.strNOG.ENOG411BR1D.fasta
--- a/trimal_repo/dataset/example.086.AA.strNOG.ENOG411BR1D.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,560 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.087.AA.strNOG.ENOG411BRCH.fasta
--- a/trimal_repo/dataset/example.087.AA.strNOG.ENOG411BRCH.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,195 +0,0 @@
->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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.088.AA.strNOG.ENOG411BSXF.fasta
--- a/trimal_repo/dataset/example.088.AA.strNOG.ENOG411BSXF.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,360 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.089.AA.strNOG.ENOG411BV9B.fasta
--- a/trimal_repo/dataset/example.089.AA.strNOG.ENOG411BV9B.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,300 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.090.AA.strNOG.ENOG411BVKR.fasta
--- a/trimal_repo/dataset/example.090.AA.strNOG.ENOG411BVKR.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,31108 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.codon.fa
--- a/trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.codon.fa Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,7985 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.fasta
--- a/trimal_repo/dataset/example.091.AA.strNOG.ENOG411BWBU.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,5434 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.092.DNA.fasta
--- a/trimal_repo/dataset/example.092.DNA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,104 +0,0 @@
->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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.093.DNA.fasta
--- a/trimal_repo/dataset/example.093.DNA.fasta Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,89 +0,0 @@
->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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/example.094.DNADeg.sequential_phy
--- a/trimal_repo/dataset/example.094.DNADeg.sequential_phy Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,157 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/matrix.BLOSUM62
--- a/trimal_repo/dataset/matrix.BLOSUM62 Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/dataset/matrix.Degenerated_DNA
--- a/trimal_repo/dataset/matrix.Degenerated_DNA Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
-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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/check_codon_alignments.py
--- a/trimal_repo/scripts/check_codon_alignments.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,107 +0,0 @@
-#!/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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py
--- a/trimal_repo/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,143 +0,0 @@
-#!/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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/get_sequence_representative_from_alignment.py
--- a/trimal_repo/scripts/get_sequence_representative_from_alignment.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,95 +0,0 @@
-#!/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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/get_sequences_gaps_ratio.py
--- a/trimal_repo/scripts/get_sequences_gaps_ratio.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,78 +0,0 @@
-#!/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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/remove_shorter_sequences.py
--- a/trimal_repo/scripts/remove_shorter_sequences.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,73 +0,0 @@
-#!/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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py
--- a/trimal_repo/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,273 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/scripts/set_manual_boundaries.py
--- a/trimal_repo/scripts/set_manual_boundaries.py Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,198 +0,0 @@
-#!/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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/alignment.cpp
--- a/trimal_repo/source/alignment.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,3378 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/alignment.h
--- a/trimal_repo/source/alignment.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,546 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/autAlignment.cpp
--- a/trimal_repo/source/autAlignment.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,448 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/compareFiles.cpp
--- a/trimal_repo/source/compareFiles.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,518 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/compareFiles.h
--- a/trimal_repo/source/compareFiles.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,51 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/defines.h
--- a/trimal_repo/source/defines.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,54 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/main.cpp
--- a/trimal_repo/source/main.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1973 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/makefile
--- a/trimal_repo/source/makefile Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,50 +0,0 @@
-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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/makefile.MacOS
--- a/trimal_repo/source/makefile.MacOS Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,53 +0,0 @@
-## 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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/readAl.cpp
--- a/trimal_repo/source/readAl.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,383 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/rwAlignment.cpp
--- a/trimal_repo/source/rwAlignment.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2253 +0,0 @@\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 << "<span id=" << type << ">" << sequences[i][k] << "</span>";\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/sequencesMatrix.cpp
--- a/trimal_repo/source/sequencesMatrix.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,209 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/sequencesMatrix.h
--- a/trimal_repo/source/sequencesMatrix.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,117 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/similarityMatrix.cpp
--- a/trimal_repo/source/similarityMatrix.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,463 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/similarityMatrix.h
--- a/trimal_repo/source/similarityMatrix.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,70 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statAl.cpp
--- a/trimal_repo/source/statAl.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,574 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statisticsConservation.cpp
--- a/trimal_repo/source/statisticsConservation.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,428 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statisticsConservation.h
--- a/trimal_repo/source/statisticsConservation.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,112 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statisticsFiles.cpp
--- a/trimal_repo/source/statisticsFiles.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,56 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statisticsFiles.h
--- a/trimal_repo/source/statisticsFiles.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,48 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statisticsGaps.cpp
--- a/trimal_repo/source/statisticsGaps.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,464 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/statisticsGaps.h
--- a/trimal_repo/source/statisticsGaps.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,87 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/utils.cpp
--- a/trimal_repo/source/utils.cpp Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,850 +0,0 @@\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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/utils.h
--- a/trimal_repo/source/utils.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,207 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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 b15a3147e604 -r 98944ec4bfc7 trimal_repo/source/values.h
--- a/trimal_repo/source/values.h Fri Mar 25 17:10:43 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,119 +0,0 @@
-/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
-
-    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