# 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 - - - clustalo - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - getTree == "--guidetree-out=guidetree.txt" - - - - - - - - - - - - - - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + getTree == "--guidetree-out=guidetree.txt" + + + + + + + + + + + + + + + + + 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 @@ - - - - - -