# HG changeset patch
# User dcorreia
# Date 1486387270 18000
# Node ID 23cba68908b6bb10f140c495ede39ec7bbb659d3
# Parent 2a218f19a2a0bb64b66dacb2856616ff7de2425f
planemo upload commit e0ca504b3313992020acf8ab7aed0a261237766e-dirty
diff -r 2a218f19a2a0 -r 23cba68908b6 clustalo.xml
--- a/clustalo.xml Thu Jan 26 09:35:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,220 +0,0 @@
-
- Multiple sequence alignment software
-
- operation_0499
- operation_0492
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- clustalo
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- getTree == "--guidetree-out=guidetree.txt"
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- Multiple sequence input file (- for stdin)
- --hmm-in= HMM input files
- --dealign Dealign input sequences
- --profile1, --p1= Pre-aligned multiple sequence file (aligned columns will be kept fix)
- --profile2, --p2= Pre-aligned multiple sequence file (aligned columns will be kept fix)
- --is-profile Disable check if profile, force profile (default no)
- -t, --seqtype *Protein, RNA, DNA* Force a sequence type (default: auto)
- --infmt *fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]*. Forced sequence input file format (default: auto)
-
------
-
-Clustering:
- --distmat-in= Pairwise distance matrix input file (skips distance computation)
- --distmat-out= Pairwise distance matrix output file
- --guidetree-in= Guide tree input file (skips distance computation and guide-tree clustering step)
- --guidetree-out= Guide tree output file
- --pileup Sequentially align sequences
- --full Use full distance matrix for guide-tree calculation (might be slow; mBed is default)
- --full-iter Use full distance matrix for guide-tree calculation during iteration (might be slowish; mBed is default)
- --cluster-size= soft maximum of sequences in sub-clusters
- --clustering-out= Clustering output file
- --trans= Use transitivity (default: 0)
- --posterior-out= Posterior probability output file
- --use-kimura Use Kimura distance correction for aligned sequences (default no)
- --percent-id convert distances into percent identities (default no)
-
-----
-
-Alignment Output:
- -o, --outfile= Multiple sequence alignment output file (default: stdout)
- --outfmt *fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]* MSA output file format (default: fasta)
- --residuenumber, --resno in Clustal format print residue numbers (default no)
- --wrap= number of residues before line-wrap in output
- --output-order *input-order, tree-order* MSA output order like in input/guide-tree
-
-----
-
-Iteration:
- --iterations, --iter= Number of (combined guide-tree/HMM) iterations
- --max-guidetree-iterations= Maximum number of guidetree iterations
- --max-hmm-iterations= Maximum number of HMM iterations
-
-----
-
-Limits (will exit early, if exceeded):
- --maxnumseq= Maximum allowed number of sequences
- --maxseqlen= Maximum allowed sequence length
-
-----
-
-Miscellaneous:
- --auto Set options automatically (might overwrite some of your options)
- --threads= Number of processors to use
- --pseudo= Input file for pseudo-count parameters
- -l, --log= Log all non-essential output to this file
- -h, --help Print this help and exit
- -v, --verbose Verbose output (increases if given multiple times)
- --version Print version information and exit
- --long-version Print long version information and exit
- --force Force file overwriting
- ]]>
-
-
- 10.1038/msb.2011.75
-
-
diff -r 2a218f19a2a0 -r 23cba68908b6 clustalo/clustalo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalo/clustalo.xml Mon Feb 06 08:21:10 2017 -0500
@@ -0,0 +1,220 @@
+
+ Multiple sequence alignment software
+
+ operation_0499
+ operation_0492
+
+
+ clustalo
+
+
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+
+
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+ getTree == "--guidetree-out=guidetree.txt"
+
+
+
+
+
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+
+
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+
+
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+
+
+ Multiple sequence input file (- for stdin)
+ --hmm-in= HMM input files
+ --dealign Dealign input sequences
+ --profile1, --p1= Pre-aligned multiple sequence file (aligned columns will be kept fix)
+ --profile2, --p2= Pre-aligned multiple sequence file (aligned columns will be kept fix)
+ --is-profile Disable check if profile, force profile (default no)
+ -t, --seqtype *Protein, RNA, DNA* Force a sequence type (default: auto)
+ --infmt *fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]*. Forced sequence input file format (default: auto)
+
+-----
+
+Clustering:
+ --distmat-in= Pairwise distance matrix input file (skips distance computation)
+ --distmat-out= Pairwise distance matrix output file
+ --guidetree-in= Guide tree input file (skips distance computation and guide-tree clustering step)
+ --guidetree-out= Guide tree output file
+ --pileup Sequentially align sequences
+ --full Use full distance matrix for guide-tree calculation (might be slow; mBed is default)
+ --full-iter Use full distance matrix for guide-tree calculation during iteration (might be slowish; mBed is default)
+ --cluster-size= soft maximum of sequences in sub-clusters
+ --clustering-out= Clustering output file
+ --trans= Use transitivity (default: 0)
+ --posterior-out= Posterior probability output file
+ --use-kimura Use Kimura distance correction for aligned sequences (default no)
+ --percent-id convert distances into percent identities (default no)
+
+----
+
+Alignment Output:
+ -o, --outfile= Multiple sequence alignment output file (default: stdout)
+ --outfmt *fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]* MSA output file format (default: fasta)
+ --residuenumber, --resno in Clustal format print residue numbers (default no)
+ --wrap= number of residues before line-wrap in output
+ --output-order *input-order, tree-order* MSA output order like in input/guide-tree
+
+----
+
+Iteration:
+ --iterations, --iter= Number of (combined guide-tree/HMM) iterations
+ --max-guidetree-iterations= Maximum number of guidetree iterations
+ --max-hmm-iterations= Maximum number of HMM iterations
+
+----
+
+Limits (will exit early, if exceeded):
+ --maxnumseq= Maximum allowed number of sequences
+ --maxseqlen= Maximum allowed sequence length
+
+----
+
+Miscellaneous:
+ --auto Set options automatically (might overwrite some of your options)
+ --threads= Number of processors to use
+ --pseudo= Input file for pseudo-count parameters
+ -l, --log= Log all non-essential output to this file
+ -h, --help Print this help and exit
+ -v, --verbose Verbose output (increases if given multiple times)
+ --version Print version information and exit
+ --long-version Print long version information and exit
+ --force Force file overwriting
+ ]]>
+
+
+ 10.1038/msb.2011.75
+
+
diff -r 2a218f19a2a0 -r 23cba68908b6 clustalo/test-data/seqtest.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalo/test-data/seqtest.fasta Mon Feb 06 08:21:10 2017 -0500
@@ -0,0 +1,35 @@
+>TestSequence1
+ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
+YVKQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGERAA
+AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYVQDVCA
+SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL
+GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQLL
+KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR
+>TestSequence2
+ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
+YAQKLLYKDALAECCSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGERHGDLC
+AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD
+SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCKNYAEAKDVFLVC
+GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPDEL
+NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQPTLVEVSRNLGKVGTKCCSLAEGERVCA
+>TestSequence3
+ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYA
+YANKYNGVFQECCQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGERHGDLVCA
+ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD
+TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCKNYQEAKDAFLVC
+GSFLYEYSRRHPEYVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQVFL
+NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER
+>TestSequence4
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERHGDLVCA
+AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD
+SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLVC
+GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL
+NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR
+>TestSequence5
+ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
+YAEEYKGVFTECCEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGERHGDLVFL
+AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD
+SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCKNYQEAKDVFLVC
+GTFLYEYSRRHPSSVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPHNQD
+NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER
\ No newline at end of file
diff -r 2a218f19a2a0 -r 23cba68908b6 clustalo/test-data/seqtest_aln.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalo/test-data/seqtest_aln.fasta Mon Feb 06 08:21:10 2017 -0500
@@ -0,0 +1,40 @@
+>TestSequence1
+ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
+YV--KQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER
+AA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAK
+YVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYK
+EAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQ
+PLVDEPQL-LKLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGN
+KCCTLPESKR---
+>TestSequence2
+ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
+YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER
+HGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGK
+YMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYA
+EAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELK
+PLIDEPDE-LNLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGT
+KCCSLAEGERVCA
+>TestSequence3
+ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
+AY-ANKYNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER
+HGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAK
+YICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQ
+EAKDAFLVCGSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLK
+HLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGT
+RCCTKPESER---
+>TestSequence4
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+-F-AKRYKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER
+HGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAK
+YICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYA
+EAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFK
+PLVEEPQL-LNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGS
+KCCKHPEAKR---
+>TestSequence5
+ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
+-Y-AEEYKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER
+HGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAK
+YICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQ
+EAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFK
+PLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGS
+KCCTHPEAER---
diff -r 2a218f19a2a0 -r 23cba68908b6 clustalo/test-data/seqtest_aln2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalo/test-data/seqtest_aln2.fasta Mon Feb 06 08:21:10 2017 -0500
@@ -0,0 +1,40 @@
+>TestSequence1
+ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
+YV--KQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER
+AA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAK
+YVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYK
+EAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQ
+PLVDEPQL-LKLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGN
+KCCTLPESKR---
+>TestSequence2
+ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
+YAQKLLYKDALAECC-----SAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER
+HGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGK
+YMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYA
+EAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELK
+PLIDEPDE-LNLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGT
+KCCSLAEGERVCA
+>TestSequence3
+ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
+AYA-NKYNGVFQECC-----QAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER
+HGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAK
+YICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQ
+EAKDAFLVCGSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLK
+HLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGT
+RCCTKPESER---
+>TestSequence4
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+F-A-KRYKAAFTECC-----QAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER
+HGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAK
+YICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYA
+EAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFK
+PLVEEPQL-LNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGS
+KCCKHPEAKR---
+>TestSequence5
+ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
+Y-A-EEYKGVFTECC-----EAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER
+HGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAK
+YICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQ
+EAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFK
+PLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGS
+KCCTHPEAER---
diff -r 2a218f19a2a0 -r 23cba68908b6 clustalo/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalo/tool_dependencies.xml Mon Feb 06 08:21:10 2017 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+
diff -r 2a218f19a2a0 -r 23cba68908b6 test-data/seqtest.fasta
--- a/test-data/seqtest.fasta Thu Jan 26 09:35:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
->TestSequence1
-ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
-YVKQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGERAA
-AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYVQDVCA
-SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL
-GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQLL
-KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR
->TestSequence2
-ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
-YAQKLLYKDALAECCSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGERHGDLC
-AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD
-SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCKNYAEAKDVFLVC
-GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPDEL
-NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQPTLVEVSRNLGKVGTKCCSLAEGERVCA
->TestSequence3
-ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYA
-YANKYNGVFQECCQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGERHGDLVCA
-ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD
-TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCKNYQEAKDAFLVC
-GSFLYEYSRRHPEYVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQVFL
-NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER
->TestSequence4
-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
-FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERHGDLVCA
-AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD
-SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLVC
-GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL
-NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR
->TestSequence5
-ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
-YAEEYKGVFTECCEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGERHGDLVFL
-AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD
-SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCKNYQEAKDVFLVC
-GTFLYEYSRRHPSSVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPHNQD
-NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER
\ No newline at end of file
diff -r 2a218f19a2a0 -r 23cba68908b6 test-data/seqtest_aln.fasta
--- a/test-data/seqtest_aln.fasta Thu Jan 26 09:35:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
->TestSequence1
-ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
-YV--KQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER
-AA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAK
-YVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYK
-EAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQ
-PLVDEPQL-LKLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGN
-KCCTLPESKR---
->TestSequence2
-ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
-YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER
-HGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGK
-YMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYA
-EAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELK
-PLIDEPDE-LNLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGT
-KCCSLAEGERVCA
->TestSequence3
-ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
-AY-ANKYNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER
-HGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAK
-YICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQ
-EAKDAFLVCGSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLK
-HLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGT
-RCCTKPESER---
->TestSequence4
-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
--F-AKRYKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER
-HGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAK
-YICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYA
-EAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFK
-PLVEEPQL-LNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGS
-KCCKHPEAKR---
->TestSequence5
-ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
--Y-AEEYKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER
-HGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAK
-YICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQ
-EAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFK
-PLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGS
-KCCTHPEAER---
diff -r 2a218f19a2a0 -r 23cba68908b6 test-data/seqtest_aln2.fasta
--- a/test-data/seqtest_aln2.fasta Thu Jan 26 09:35:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
->TestSequence1
-ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
-YV--KQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER
-AA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAK
-YVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYK
-EAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQ
-PLVDEPQL-LKLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGN
-KCCTLPESKR---
->TestSequence2
-ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
-YAQKLLYKDALAECC-----SAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER
-HGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGK
-YMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYA
-EAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELK
-PLIDEPDE-LNLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGT
-KCCSLAEGERVCA
->TestSequence3
-ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
-AYA-NKYNGVFQECC-----QAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER
-HGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAK
-YICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQ
-EAKDAFLVCGSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLK
-HLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGT
-RCCTKPESER---
->TestSequence4
-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
-F-A-KRYKAAFTECC-----QAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER
-HGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAK
-YICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYA
-EAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFK
-PLVEEPQL-LNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGS
-KCCKHPEAKR---
->TestSequence5
-ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
-Y-A-EEYKGVFTECC-----EAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER
-HGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAK
-YICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQ
-EAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFK
-PLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGS
-KCCTHPEAER---
diff -r 2a218f19a2a0 -r 23cba68908b6 tool_dependencies.xml
--- a/tool_dependencies.xml Thu Jan 26 09:35:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
-
-
-