# HG changeset patch
# User iuc
# Date 1731661166 0
# Node ID ebe28cac8d8bb5b47038ebbf2fb3ec7e9779784e
planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
diff -r 000000000000 -r ebe28cac8d8b README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,3 @@
+# trimAl
+
+[trimAl](https://github.com/inab/trimal), a tool for automated alignment trimming in large-scale phylogenetic analyses.
diff -r 000000000000 -r ebe28cac8d8b test-data/custom_trimmed_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.html Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,74 @@
+
+
+
+ trimAl v1.5.0 Summary
+
+
+
+
+
+ Selected Sequences: 9 /Selected Residues: 63
+ Deleted Sequences: 0 /Deleted Residues: 122
+
+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1=
+ Similarity Scores: =0= <1e-6 <1e-5 <1e-4 <.001 <.010 <.100 <.250 <.500 <.750 <1.00 =1=
+
+ 10 20 30 40 50 60 70 80 90 100 110 120
+ =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+
+ Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL
+ Xtr21234 ----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQSKEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL
+ LcaH ----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQSHEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL
+ Hsa167996 MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL
+ Mmu024661 MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL
+ Dre37936 ---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNSEEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL
+ LcaM ----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENSDEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL
+ Tru14292 ----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENSDEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL
+ Ola20972 ----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENSHEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL
+
+ Selected Cols:
+
+ Gaps Scores:
+ Similarity Scores:
+
+ 130 140 150 160 170 180
+ =========+=========+=========+=========+=========+=========+=====
+ Csa004271 HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS-----
+ Xtr21234 HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS------
+ LcaH HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGKES--S
+ Hsa167996 HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES
+ Mmu024661 HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGHGD-ES
+ Dre37936 HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS-----
+ LcaM HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGGKS---
+ Tru14292 HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGSKS---
+ Ola20972 HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS---
+
+ Selected Cols:
+
+ Gaps Scores:
+ Similarity Scores:
+
+
+
diff -r 000000000000 -r ebe28cac8d8b test-data/custom_trimmed_example.009.AA.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.phy Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,11 @@
+ 9 63
+Csa004271 --------------YMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Xtr21234 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaH SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Hsa167996 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Mmu024661 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Dre37936 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaM SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Tru14292 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Ola20972 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+
diff -r 000000000000 -r ebe28cac8d8b test-data/example.004.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.004.AA.fasta Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,18 @@
+>Sp8
+FPWNGLQIHMMGIII
+
+>Sp17
+FPWNGLQIHMMGIII
+
+>Sp10
+FPWNGLQIHMMGIII
+
+>Sp26
+FPWNGLQIHMMGIII
+
+>Sp33
+FPWNGLQIHMMGIII
+
+>Sp6
+FPWNGLQIHMMGIII
+
diff -r 000000000000 -r ebe28cac8d8b test-data/example.009.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.009.AA.fasta Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,45 @@
+>Csa004271
+---------------------------------MYMAMGHFFDRDDVALKNISEYFKECS
+EEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL
+HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS
+-----
+>Xtr21234
+----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQS
+KEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL
+HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS-
+-----
+>LcaH
+----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQS
+HEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL
+HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGK
+ES--S
+>Hsa167996
+MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL
+HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGD
+SDNES
+>Mmu024661
+MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL
+HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGH
+GD-ES
+>Dre37936
+---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNS
+EEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL
+HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS
+-----
+>LcaM
+----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENS
+DEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL
+HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGG
+KS---
+>Tru14292
+----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENS
+DEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL
+HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGS
+KS---
+>Ola20972
+----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENS
+HEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL
+HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGS
+KS---
\ No newline at end of file
diff -r 000000000000 -r ebe28cac8d8b test-data/trimmed_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_example.009.AA.html Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,71 @@
+
+
+
+ trimAl v1.5.0 Summary
+
+
+
+
+
+ Selected Sequences: 9 /Selected Residues: 174
+ Deleted Sequences: 0 /Deleted Residues: 11
+
+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1=
+
+ 10 20 30 40 50 60 70 80 90 100 110 120
+ =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+
+ Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL
+ Xtr21234 ----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQSKEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL
+ LcaH ----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQSHEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL
+ Hsa167996 MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL
+ Mmu024661 MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL
+ Dre37936 ---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNSEEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL
+ LcaM ----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENSDEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL
+ Tru14292 ----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENSDEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL
+ Ola20972 ----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENSHEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL
+
+ Selected Cols:
+
+ Gaps Scores:
+
+ 130 140 150 160 170 180
+ =========+=========+=========+=========+=========+=========+=====
+ Csa004271 HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS-----
+ Xtr21234 HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS------
+ LcaH HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGKES--S
+ Hsa167996 HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES
+ Mmu024661 HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGHGD-ES
+ Dre37936 HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS-----
+ LcaM HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGGKS---
+ Tru14292 HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGSKS---
+ Ola20972 HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS---
+
+ Selected Cols:
+
+ Gaps Scores:
+
+
+
diff -r 000000000000 -r ebe28cac8d8b test-data/trimmed_example.009.AA.mega
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_example.009.AA.mega Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,58 @@
+#MEGA
+!Title ./test-data/example.009.AA.fasta;
+!Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard;
+
+#Csa004271
+---------- ---------- ---------M YMAMGHFFDR DDVALKNISE
+YFKECSEEER EHANKMIEFH NKRGGTTTYF PIKAPGSFDP ANTIKAMNCA
+LALEVNVNKS LLALHE--TA NGDPEFQDFI EANFLHEQVD AIKKLKDYIT
+NLKLVG---T GLGEFLFDKH FKSS
+
+#Xtr21234
+MISQVRQNYS HDCEAAVNRM VNLEMYASYT YLSMSHYFDR DDVALHHVAE
+FFKEQSKEER ECAEKLMKCQ NKRGGRIVLQ DIKKPERDEW GSTLDAMQTA
+LDLEKHVNQA LLDLHNLATE RKDPHICDFL ESEHLDEQVK HMKKFGDHIT
+NLKRLGVPQN GMGEYLFDKH SLS-
+
+#LcaH
+MSSQVRQNFH QDCEAAINRQ INLELYASYV YLSMAYYFDR DDQALHNFAK
+FFRHQSHEER EHAEKLMKLQ NQRGGRIFLQ DVRKPDRDEW GSGVEALECA
+LQLEKSVNQS LLDLHKLCSD HNDPHLCDFI ETHYLDEQVK SIKELADWVT
+NLRRMGAPQN GMAEYLFDKH TLGK
+
+#Hsa167996
+STSQVRQNYH QDSEAAINRQ INLELYASYV YLSMSYYFDR DDVALKNFAK
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDCDDW ESGLNAMECA
+LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT
+NLRKMGAPES GLAEYLFDKH TLGD
+
+#Mmu024661
+SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDDW ESGLNAMECA
+LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT
+NLRKMGAPEA GMAEYLFDKH TLGH
+
+#Dre37936
+ETSQIRQNYV RDCEAAINKM INLELYAGYT YTSMAHYFKR DDVALPGFAK
+FFKKNSEEER EHAEKFMEFQ NKRGGRIVLQ DIKKPDRDVW GNGLIAMQCA
+LQLEKNVNQA LLDLHKLATE MGDPHLCDFL ETHYLNEQVE AIKKLGDHIT
+NLSKMDAGNN RMAEYLFDKH TLDS
+
+#LcaM
+MESQVRQNYH RDCEAAVNRM VNMEMFASYT YTSMAFYFSR DDVALPGFSH
+FFKENSDEER EHAEKLLSFQ NKRGGHIFLQ DIKKPERDEW GSGLEAMQCA
+LQLKKNVNQA LLDLHKLASD HGDPHLCDFL ETHYLNEQVE AIKKLGDYIS
+NLSRMDAQKN KMAEYLFDKH SLGG
+
+#Tru14292
+MESQVRQNYH RDCEAAINKM INMELYASYT YTSMAFFFSR DDVALPGFAH
+FFKENSDEER EHAEKLLSFQ NKRGGRIFLQ DIKKPERDEW GSGLEAMQCA
+LQLEKKVNQA LLDLHKLASD HVDPHLCDFL ESHYLNEQVE AIKKLGDYIT
+NLSRMDAQNN KMAEYLFDKH TLGS
+
+#Ola20972
+MESQVRQNYH RDCEAAINRM VNMELFASYT YTSMAFYFDR DDVALPGFSH
+FFKENSHEEK EHADKLLSFQ NKRGGRIFLQ DVKKPERDEW GSGLEAMQCA
+LQLEKNVNQA LLDLHKVASD HKDPHMCDFL ETHYLNEQVE SIKKIGDHIT
+NLTRMDAHTN KMAEYLFDKH TLGS
+
diff -r 000000000000 -r ebe28cac8d8b trimal.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal.xml Fri Nov 15 08:59:26 2024 +0000
@@ -0,0 +1,131 @@
+
+ for automated alignment trimming
+
+ 1.5
+ 0
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+ trimal
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+ trimal
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+ doi:10.1093/bioinformatics/btp348
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\ No newline at end of file