| Previous changeset 6:c5908940967d (2017-11-11) Next changeset 8:4de39704d423 (2021-03-13) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71" |
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modified:
mafft.xml test-data/mafft_fftns_result.aln test-data/mafft_nwns_result.aln |
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added:
macros.xml mafft-add.xml test-data/add_seq.fa test-data/mafft_add_result.aln test-data/mafft_custom_result.aln |
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| diff -r c5908940967d -r aaefa93c2dd2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 15 15:33:37 2020 -0400 |
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| @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">1</token> + <token name="@TOOL_VERSION@">7.455</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="7.455">mafft</requirement> + <requirement type="package" version="36.3.8">fasta3</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/molbev/mst010</citation> + </citations> + </xml> +</macros> |
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| diff -r c5908940967d -r aaefa93c2dd2 mafft-add.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mafft-add.xml Wed Apr 15 15:33:37 2020 -0400 |
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| @@ -0,0 +1,88 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION@"> + <description>Align a sequence,alignment or fragments to an existing alignment.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + </stdio> + <version_command> <![CDATA[ + mafft --version + ]]> + </version_command> + <command> + <![CDATA[ + mafft + #if $sequences.sequenceType == 'singleseq' + $sequences.preservegap '$inputSequences' + #elif $sequences.sequenceType == 'frags' + --addfragments '$inputSequences' + #elif $sequences.sequenceType == 'group' + --addprofile '$inputSequences' + #end if + $keeplength $map $reorder + '$inputAlignment' + > '$outputAlignment' + #if $map == '--mapout' + && mv '${inputSequences}.map' '$outputmap' + #end if + ]]> + </command> + <inputs> + <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/> + <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/> + <conditional name="sequences"> + <param name="sequenceType" type="select" label="What do you want to add to the alignment" > + <option value="singleseq">A single sequence</option> + <option value="frags" selected="true">Fragments</option> + <option value="group">An alignment</option> + </param> + <when value='singleseq'> + <param name="preservegap" type="select" label="Preserve the original alignment" help="Keep the given alignment unchanged (--add .)If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved (--seed)"> + <option value="--add" selected="true" >Yes</option> + <option value="--seed">no</option> + </param> + </when> + <when value='frags'/> + <when value='group'/> + </conditional> + <param name="keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged. Insertions at the additional sequences are deleted" /> + <param name="map" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of positions (--mapout)" help="Output a correspondence table of positions, sequence.map, between before and after the calculation. The --mapout option automatically turns on the --keeplength option, to keep the numbering of sites in the reference alignment" /> + <param name="reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences (--reorder)" /> + </inputs> + <outputs> + <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/> + <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions "> + <filter>map == True</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1" > + <param name="inputSequences" value="add_seq.fa"/> + <param name="inputAlignment" value="mafft_fftns_result.aln"/> + <param name="sequenceType" value="singleseq"/> + <param name="preservegap" value="--add"/> + <param name="keeplength" value="--keeplength"/> + <param name="map" value=""/> + <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/> + </test> + </tests> + <help> + <![CDATA[ +Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement. + +- Sequences in new_sequences are ungapped and then aligned to existing_alignment. +- new_sequences is a single multi-FASTA format file. +- existing_alignment is a single multi-FASTA format file. +- Gaps in existing_alignment are preserved by default (--add), but it can be deactivated (--seed). In that case the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved. +- The alignment length may be conserved if the --keeplength option is given. The alignment length is unchanged. Insertions at the new sequences are deleted. +- --mapout options output a correspondence table of positions, new_sequences.map, between before and after the calculation. The --mapout option automatically turns on the --keeplength option, to keep the numbering of sites in the reference alignment. +- Omit --reorder to preserve the original sequence order. + + ]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r c5908940967d -r aaefa93c2dd2 mafft.xml --- a/mafft.xml Sat Nov 11 15:06:34 2017 -0500 +++ b/mafft.xml Wed Apr 15 15:33:37 2020 -0400 |
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| b'@@ -1,229 +1,294 @@\n-<tool id="rbc_mafft" name="MAFFT" version="7.221.3">\n- <description>Multiple alignment program for amino acid or nucleotide sequences</description>\n- <requirements>\n- <requirement type="package" version="7.221">mafft</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />\n- <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />\n- </stdio>\n- <version_command>\n- <![CDATA[\n- mafft --version\n- ]]>\n- </version_command>\n- <command>\n- <![CDATA[\n- #if $cond_flavour.flavourType != \'custom\'\n- $cond_flavour.flavourType\n- #elif $cond_flavour.flavourType == \'custom\'\n- ### full parameter options\n- mafft\n- $cond_flavour.distance_method\n- --retree $cond_flavour.retree\n- --maxiterate $cond_flavour.iterations\n- #end if\n-\n- ## specify threads to use\n- --thread \\${GALAXY_SLOTS:-1}\n-\n- $datatype\n- --ep $ep\n- --op $op\n- $adjustdirection\n- \n- #if $matrix_condition.matrix == "BLOSUM"\n- --bl ${matrix_condition.BLOSUM}\n- #elif $matrix_condition.matrix == "PAM"\n- --jtt ${matrix_condition.PAM}\n- #end if\n-\n- $reorder\n- $getTree\n- $outputFormat\n- $inputSequences > $outputAlignment;\n-\n- #if $getTree == "--treeout"\n- mv ${inputSequences}.tree $outputTree;\n- #end if\n- ]]>\n- </command>\n- <inputs>\n- <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>\n- <param name="datatype" type="select" label="Data type">\n- <option value="">Auto detection</option>\n- <option value="--nuc">Nucleic acids</option>\n- <option value="--amino">Amino acids</option>\n- </param>\n- <conditional name="cond_flavour">\n- <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">\n- <option value="mafft --auto">auto</option>\n- <option value="mafft-fftns" selected="true">fftns</option>\n- <option value="mafft-fftnsi">fftnsi</option>\n- <option value="mafft-nwns">nwns</option>\n- <option value="mafft-nwnsi">nwnsi</option>\n- <option value="mafft-einsi">einsi</option>\n- <option value="mafft-ginsi">ginsi</option>\n- <option value="mafft-linsi">linsi</option>\n- <option value="mafft-qinsi">qinsi</option>\n- <option value="mafft-xinsi">xinsi</option>\n- <option value="custom">Custom Parameters</option>\n- </param>\n- <when value="mafft-fftns"/>\n- <when value="mafft --auto"/>\n- <when value="mafft-fftnsi"/>\n- <when value="mafft-nwns"/>\n- <when value="mafft-nwnsi"/>\n- <when value="mafft-einsi"/>\n- <when value="mafft-ginsi"/>\n- <when value="mafft-linsi"/>\n- <when value="mafft-qinsi"/>\n- <when value="mafft-xinsi"/>\n- <when value="custom">\n- <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">\n- <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>\n- <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>\n- <option value="--localpair">Local alignment (Smith-Waterman)</option>\n- <option value="--genafpair">Local, affine gap cost</option>\n- </param>\n- '..b'putSequences" value="sample.fa"/>\r\n+ <param name="flavourType" value="mafft-nwns"/>\r\n+ <param name="outputFormat" value="--clustalout"/>\r\n+ <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln"/>\r\n+ </test>\r\n+ <test expect_num_outputs="1" >\r\n+ <param name="inputSequences" value="sample.fa"/>\r\n+ <param name="flavourType" value="custom"/>\r\n+ <param name="matrix_condition" value="BLOSUM"/>\r\n+ <param name="BLOSUM" value="62"/>\r\n+ <param name="distance_method" value="--fastapair"/>\r\n+ <param name="weighti" value="2.7"/>\r\n+ <param name="iterations" value="1000"/>\r\n+ <param name="outputFormat" value="--clustalout"/>\r\n+ <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln"/>\r\n+ </test>\r\n+ </tests>\r\n+ <help> <![CDATA[\r\n+ **What it does**\r\n+ MAFFT is a multiple sequence alignment program for unix-like operating systems.\r\n+ It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <\xe2\x88\xbc200 sequences),\r\n+ FFT-NS-2 (fast; for alignment of <\xe2\x88\xbc30,000 sequences), etc.\r\n+ From the MAFFT man page, an overview of the different predefined flavours of the tool.\r\n+ **Accuracy-oriented methods:**\r\n+ - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):\r\n+ - mafft --localpair --maxiterate 1000 input [> output]\r\n+ - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):\r\n+ - mafft --globalpair --maxiterate 1000 input [> output]\r\n+ - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):\r\n+ - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.\r\n+ **Speed-oriented methods:**\r\n+ - FFT-NS-i (iterative refinement method; two cycles only):\r\n+ - mafft --retree 2 --maxiterate 2 input [> output]\r\n+ - FFT-NS-i (iterative refinement method; max. 1000 iterations):\r\n+ - mafft --retree 2 --maxiterate 1000 input [> output]\r\n+ - FFT-NS-2 (fast; progressive method):\r\n+ - mafft --retree 2 --maxiterate 0 input [> output]\r\n+ - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):\r\n+ - mafft --retree 1 --maxiterate 0 input [> output]\r\n+ - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):\r\n+ - mafft --retree 2 --maxiterate 2 --nofft input [> output]\r\n+ - NW-NS-2 (fast; progressive method without the FFT approximation):\r\n+ - mafft --retree 2 --maxiterate 0 --nofft input [> output]\r\n+ - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):\r\n+ - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]\r\n+\r\n+ **Options:**\r\n+ --auto\r\n+ Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)\r\n+ --adjustdirection\r\n+ Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.\r\n+ --op\r\n+ Gap opening penalty, default: 1.53\r\n+ --ep\r\n+ Offset (works like gap extension penalty), default: 0.0\r\n+ --maxiterate\r\n+ Maximum number of iterative refinement, default: 0\r\n+ --clustalout\r\n+ Output: clustal format, default: fasta\r\n+ --thread\r\n+ Number of threads (if unsure, --thread -1)\r\n+ --retree number\r\n+ Guide tree is built number times in the progressive stage.\r\n+ Valid with 6mer distance. Default: 2\r\n+ ]]>\r\n+ </help>\r\n+ <expand macro="citations" />\r\n+</tool>\r\n' |
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| diff -r c5908940967d -r aaefa93c2dd2 test-data/add_seq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/add_seq.fa Wed Apr 15 15:33:37 2020 -0400 |
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| @@ -0,0 +1,2 @@ +> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91] +MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF |
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| diff -r c5908940967d -r aaefa93c2dd2 test-data/mafft_add_result.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_add_result.aln Wed Apr 15 15:33:37 2020 -0400 |
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| b"@@ -0,0 +1,481 @@\n+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n+----------------------------------------MNG----------------T\n+E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL\n+AAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSM\n+N-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHAIM\n+GVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMF\n+VVHFLVPFVIIFFCYGRLLCTV----KEAAAAQQ--------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-H\n+QGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC--------GKNPL\n+GDDE--SGASTSKTEVSSVS-TSPVSPA--------------------------------\n+---------------------------------------------------------\n+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n+----------------------------------------MNG----------------T\n+E--G--PNFYVP----FSNITGVVRSPFEQPQY-------YLAEPWQ---------FSML\n+AAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSL\n+H-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHAIM\n+GVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMF\n+VVHFTIPMIVIFFCYGQLVFTV----KEAAAQQQ--------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-H\n+QGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC--------GKNPL\n+GDDE--ASATASKTE------TSQVAPA--------------------------------\n+---------------------------------------------------------\n+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n+----------------------------------------MNG----------------T\n+E--G--INFYVP----MSNKTGVVRSPFEYPQY-------YLAEPWK---------YRLV\n+CCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAW\n+N-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHAMM\n+GIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMF\n+VIHFIIPVVVIFFSYGRLICKV----REAAAQQQ--------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-N\n+KGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC--------GKNPF\n+GDEDVSSTVSQSKTEVSSVS-SSQVSPA--------------------------------\n+---------------------------------------------------------\n+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n+----------------------------------------MNG----------------T\n+E--G--KNFYVP----MSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKIL\n+ALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAI\n+N-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSSHAFA\n+GIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMF\n+VCHFILPVAVIFFTYGRLVCTV----KAAAAQQQ--------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-N\n+KGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC--------GKNPL\n+GDDE-SSTVSTSKTEVSS------VSPA--------------------------------\n+---------------------------------------------------------\n+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n+----------------------------------------MNG----------------T\n+E--G--NNFYVP----LSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKLL\n+AVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAI\n+N-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSTHASA\n+GIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMF\n+ICHFILPVTIIFFTYGRLVCTV----KAAAAQQQ--------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-N\n+KGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC--------GKNPL\n+GDEE-SSTVSTSKTEVSS------VSPA----"..b"-------------------------------------------\n+---------------GQGNNTTASQEPFGT-GGNVTSISDVT---------FSYQ--VIT\n+SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV\n+L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA\n+LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST\n+FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------\n+--------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG--\n+-------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG--\n+SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C\n+ESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RR----\n+------------------------------------------------------------\n+---------------------------------------------------------\n+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\n+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T\n+SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT\n+SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI\n+S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL\n+MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST\n+VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY\n+SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---\n+-------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--\n+-----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V\n+DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--\n+------------------------------------------------------------\n+---------------------------------------------------------\n+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T\n+SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT\n+SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI\n+S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL\n+MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST\n+VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY\n+SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---\n+-------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--\n+-----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V\n+DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--\n+------------------------------------------------------------\n+---------------------------------------------------------\n+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n+-MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNV------------T\n+VVPN--TTWW------------QASAPFDTPAALVRAAAK--------------------\n+AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEV\n+V-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGM\n+MIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQIFAT\n+ASSFYVPVLIILILYWRIY-------QTARKRIR--------------------------\n+-------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIA\n+AAVVAVIGRPLPTISETTTTGFTNVSS----NNTSP---EKQSCANGLEADPPTTGYGAV\n+AAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-C\n+DCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV----RRRR--\n+------A---------------PQ------------------------------------\n+---------------------------------------------------------\n+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n+----------------------------------------MNG----------------T\n+E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL\n+AAYMFFLILVGFPVNFLTLF----------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------------------------------------------------------\n" |
| b |
| diff -r c5908940967d -r aaefa93c2dd2 test-data/mafft_custom_result.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_custom_result.aln Wed Apr 15 15:33:37 2020 -0400 |
| b |
| b'@@ -0,0 +1,458 @@\n+CLUSTAL format alignment by MAFFT F-INS-i (v7.455)\n+\n+\n+1== MN------------------------GTE--GDNFYVPFS--------NKTGL-ARSPYE\n+2== MN------------------------GTE--GPNFYVPFS--------NITGV-VRSPFE\n+3== MN------------------------GTE--GINFYVPMS--------NKTGV-VRSPFE\n+4=p MN------------------------GTE--GKNFYVPMS--------NRTGL-VRSPFE\n+5=p MN------------------------GTE--GNNFYVPLS--------NRTGL-VRSPFE\n+6== MK------------------------QVPEFHEDFYIPIP-------LDINNLSAYSPFL\n+7== MR------------------------KMS--EEEFYL------------FKNISSVGPWD\n+8=opsin, ------------------------------------------------------------\n+9== MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE\n+10== MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE\n+11== MTEAWNVAVFAARRSRDD------DDTTR--GSVFTYTNT--------NN----TRGPFE\n+12== MA-AWEAA-FAARRRHEE------EDTTR--DSVFTYTNS--------NN----TRGPFE\n+13== MS----------------------SNSSQ--------------AP--PNG----TPGPFD\n+14== MESG-NV-----------------------------------------SSSLFGNVSTAL\n+15== MEYH-NV------------------------------------------SSVLGNVSSVL\n+16== MEPLCNA------------------------------------------------SEPPL\n+17== MDALCNA------------------------------------------------SEPPL\n+18== MT-------------------------------------------------------NAT\n+19== MA-------------------------------------------------------NVT\n+20== ME-------------------------------------------------SFAVAAAQL\n+21== ME-------------------------------------------------SFAVAAAQL\n+22== MD-------------------------------------------------SFAAVATQL\n+23== MERS--------------------------------------------HLPETPFDLAHS\n+24== MERS--------------------------------------------LLPEPPLAMALL\n+25== MI-------------------------------------------------------AVS\n+26== M-----------------------------------------------------------\n+27== MVESTT------------------------------------------------------\n+28== MGRD--------------------------------------------------------\n+29== MM-----DVNSSGRPDLYGH-----------LRSFLLPEVGRGLPDLSPDGGADPVAGSW\n+30== M-----------------------------------------------------------\n+31=p M-----------------------------------------------------------\n+32== MD------VLSPGQ----------------------------------GNNTTSPPAPFE\n+33=p MD------VFSFGQ----------------------------------GNNTTASQEPFG\n+34== MA------NFTFGDLALDVARMGGLASTPS------------------GLRSTGLTTPGL\n+35=p MA------NFTFGDLALDVARMGGLASTPS------------------GLRSTGLTTPGL\n+36== ME-------GAEGQEELD-------------WEALYLRL---------PLQNCSWNSTGW\n+ \n+\n+1== YP----------------------------------------------------------\n+2== QP----------------------------------------------------------\n+3== YP----------------------------------------------------------\n+4=p YP----------------------------------------------------------\n+5=p YP----------------------------------------------------------\n+6== VP----------------------------------------------------------\n+7== GP----------------------------------------------------------\n+8=opsin, ------------------------------------------------------------\n+9== GP----------------------------------------------------------\n+10== GP----------------------------------------------------------\n+11== GP----------------------------------------------------------\n+12== GP----------------------------------------------------------\n+13== GP----------------------------------------------------------\n+14== RPEARL'..b'-------------------------------------------\n+21== QSQA-TASEAE-------------------------------------------------\n+22== QSQA-TTSEAE-------------------------------------------------\n+23== ASDTETTSEAD-------------------------------------------------\n+24== PSDTETTSEAE-------------------------------------------------\n+25== STTSGTTTVTDN------------------------------------------------\n+26== SEASATTTMEEK------------------------------------------------\n+27== EEEV-VASERG--GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGA\n+28== ETEI-PAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQG-\n+29== HEALKLAERPERP-----------------EFVLQNA-----------------------\n+30== HEALKLAERPERS-----------------EFVLQNS-----------------------\n+31=p HEALKLAERPERS-----------------EFVLQNS-----------------------\n+32== ------------------------------------------------------------\n+33=p ------------------------------------------------------------\n+34== ------------------------------------------------------------\n+35=p ------------------------------------------------------------\n+36== ------------------------------------------------------------\n+ \n+\n+1== --------------------------------------------PVSP-A---\n+2== -----------------------------------------------P-A---\n+3== --------------------------------------------QVSP-A---\n+4=p -----------------------------------------------P-A---\n+5=p -----------------------------------------------P-A---\n+6== -----------------------------------------------PEK---\n+7== --------------------------------------------QVGP-N---\n+8=opsin, -----------------------------------------------------\n+9== --------------------------------------------SVSP-A---\n+10== --------------------------------------------SVSP-A---\n+11== --------------------------------------------SVAP-A---\n+12== --------------------------------------------SVSP-A---\n+13== -------------------------------------------NKVMP-AHPV\n+14== --------------------------------------------QTTA-A---\n+15== --------------------------------------------QTTA-A---\n+16== --------------------------------------------QTTA-A---\n+17== --------------------------------------------QTSA-A---\n+18== -------------------------------------------------A---\n+19== -------------------------------------------------S---\n+20== ----------------------------------------------SK-A---\n+21== ----------------------------------------------SK-A---\n+22== ----------------------------------------------SK-A---\n+23== ----------------------------------------------SK-A---\n+24== ----------------------------------------------SK-D---\n+25== -------------------------------------------EK-SN-A---\n+26== -------------------------------------------PKIPE-A---\n+27== YPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQ-A---\n+28== YPP-QGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQ-A---\n+29== -------------------------------------------DYCRKKGHDS\n+30== -------------------------------------------DHCGKKGHDT\n+31=p -------------------------------------------DHCGKKGHDT\n+32== -----------------------------------------------------\n+33=p -----------------------------------------------------\n+34== -----------------------------------------------------\n+35=p -----------------------------------------------------\n+36== -------------------------------------------------A-PQ\n+ \n' |
| b |
| diff -r c5908940967d -r aaefa93c2dd2 test-data/mafft_fftns_result.aln --- a/test-data/mafft_fftns_result.aln Sat Nov 11 15:06:34 2017 -0500 +++ b/test-data/mafft_fftns_result.aln Wed Apr 15 15:33:37 2020 -0400 |
| [ |
| b"@@ -1,504 +1,468 @@\n > 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n---------------------------------MNGTE--------------GDNF-----\n--------------YVP-----F-SNKTG----------LARSPYEYPQY-YLAEPWK---\n---------------YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMA\n-NLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIV\n-ICKPMGN-FRFGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPD\n-YYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE--------------\n-------------------------------------------------------AAAAQQ\n+----------------------------------------MNG----------------T\n+E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL\n+AAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSM\n+N-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHAIM\n+GVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMF\n+VVHFLVPFVIIFFCYGRLLCTV----KEAAAAQQ--------------------------\n ------------------------------------------------------------\n---------------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVA\n-FYIFT-HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC------\n---GKNPLGDDE--SGASTSKTEVSSVS-TSPVS---------------------------\n------------------------------------PA-----------------------\n---\n+------------------------------------------------------------\n+-------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-H\n+QGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC--------GKNPL\n+GDDE--SGASTSKTEVSSVS-TSPVSPA--------------------------------\n+---------------------------------------------------------\n > 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n---------------------------------MNGTE--------------GPNF-----\n--------------YVP-----F-SNITG----------VVRSPFEQPQY-YLAEPWQ---\n---------------FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA\n-DLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVV\n-VCKPMSN-FRFGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGID\n-YYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE--------------\n-------------------------------------------------------AAAQQQ\n+----------------------------------------MNG----------------T\n+E--G--PNFYVP----FSNITGVVRSPFEQPQY-------YLAEPWQ---------FSML\n+AAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSL\n+H-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHAIM\n+GVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMF\n+VVHFTIPMIVIFFCYGQLVFTV----KEAAAQQQ--------------------------\n ------------------------------------------------------------\n---------------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVA\n-MYIFT-HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC------\n---GKNPLGDDE--ASATASKTE------TSQVA---------------------------\n------------------------------------PA-----------------------\n---\n+------------------------------------------------------------\n+-------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-H\n+QGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC--------GKNPL\n+GDDE--ASATASKTE------TSQVAPA--------------------------------\n+---------------------------------------------------------\n > 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n---------------------------------MNGTE--------------GINF-----\n--------------YVP-----M-SNKTG----------VVRSPFEYPQY-YLAEPWK---\n---------------YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVA\n-DLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIV\n-VCKPMGN-FRFSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPD\n-YYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE--------------\n-------------------------------------------------------AAAQQQ\n+----------------------------------------MNG----------------T\n+E--G--INFYVP----MSNKTGVVRSPFEYPQY-------YLAEPWK---------YRLV\n+CCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAW\n+N-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHAMM\n+GIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMF\n+VIHFIIPVVVIFFSYGRLICKV----REAAAQQQ--------------------------\n ------------------------------------------------------------\n---------------------ESATTQ"..b'-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIA\n-LIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFG------\n----KY-RRGHR-------------------------------------------------\n+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T\n+SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT\n+SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI\n+S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL\n+MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST\n+VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY\n+SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---\n+-------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--\n+-----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V\n+DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--\n ------------------------------------------------------------\n---\n+---------------------------------------------------------\n > 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n-MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGL----------SPTG-----\n--------------LVTSD-----FNDSYGLTGQFINGSHSSRSRDNAS--ANDTSATNMT\n-DDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVA\n-DLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWA\n-VTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQD\n-K----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEE\n-TTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENAN\n-GVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAMLERQ-CNNGKKISSN\n-DTPYS-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIA\n-LIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFG------\n----KY-RRGHR-------------------------------------------------\n+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T\n+SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT\n+SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI\n+S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL\n+MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST\n+VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY\n+SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---\n+-------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--\n+-----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V\n+DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--\n ------------------------------------------------------------\n---\n+---------------------------------------------------------\n > 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n--MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGW----------EPNW-----\n--------------NVTVV-----PNTTW---------WQASAPFDTPA--ALVRAAAK--\n-------------------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVA\n-DLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWA\n-VTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQD\n-V----------GYQIFATASSFYVPVLIILILYWRIYQTARKRIR---------------\n-------------------------------RRRGATARGGVGPPP---------VPAGGA\n-LVAGGGSGGIAAAVVAVIGRPLPTISETTTTGFTNVSSNNTS---PEKQSCANGLEADPP\n-TTGYGAVAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLA\n-ILVPT-CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCG------\n----RR-VRRRR--A----------------------------------------------\n------------------------------------PQ-----------------------\n---\n+-MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNV------------T\n+VVPN--TTWW------------QASAPFDTPAALVRAAAK--------------------\n+AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEV\n+V-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGM\n+MIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQIFAT\n+ASSFYVPVLIILILYWRIY-------QTARKRIR--------------------------\n+-------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIA\n+AAVVAVIGRPLPTISETTTTGFTNVSS----NNTSP---EKQSCANGLEADPPTTGYGAV\n+AAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-C\n+DCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV----RRRR--\n+------A---------------PQ------------------------------------\n+---------------------------------------------------------\n' |
| b |
| diff -r c5908940967d -r aaefa93c2dd2 test-data/mafft_nwns_result.aln --- a/test-data/mafft_nwns_result.aln Sat Nov 11 15:06:34 2017 -0500 +++ b/test-data/mafft_nwns_result.aln Wed Apr 15 15:33:37 2020 -0400 |
| b |
| b'@@ -1,270 +1,270 @@\n-CLUSTAL format alignment by MAFFT NW-NS-2 (v7.221)\n+CLUSTAL format alignment by MAFFT NW-NS-2 (v7.455)\n \n \n-1== --------------------------------MNGTE--------------GDNF-----\n-2== --------------------------------MNGTE--------------GPNF-----\n-3== --------------------------------MNGTE--------------GINF-----\n-4=p --------------------------------MNGTE--------------GKNF-----\n-5=p --------------------------------MNGTE--------------GNNF-----\n-6== --------------------------------MKQVPEF------------HEDF-----\n-7== --------------------------------MRKMS--------------EEEF-----\n+1== ----------------------------------------MNG----------------T\n+2== ----------------------------------------MNG----------------T\n+3== ----------------------------------------MNG----------------T\n+4=p ----------------------------------------MNG----------------T\n+5=p ----------------------------------------MNG----------------T\n+6== ----------------------------------------MKQ----------------V\n+7== ----------------------------------------MRK----------------M\n 8=opsin, ------------------------------------------------------------\n-9== --------------------------------MAQQWSLQRLAGRHPQDSYEDST-----\n-10== --------------------------------MAQQWSLQRLAGRHPQDSYEDST-----\n-11== --------------------------------MTEAWNVAVFAARRSRDD-DDTT-----\n-12== --------------------------------MAA-WEAAFAARRRHEE--EDTT-----\n-13== --------------------------------MS-----------------SNSS-----\n-14== ----------MES--GNV-----------SSSLFGNVSTAL----------RPEA-----\n-15== ----------MEY--HNV-----------SSVL-GNVSSVL----------RPDA-----\n-16== ----------ME-------------------PLCNASEPPL----------RPEA-----\n-17== ----------MD-------------------ALCNASEPPL----------RPEA-----\n-18== --------------------------------MTNATGPQM----------AYYG-----\n-19== --------------------------------MANVTGPQM----------AFYG-----\n-20== ---------------MES-----------FAVAAAQLGPHF----------APLS-----\n-21== ---------------MES-----------FAVAAAQLGPHF----------APLS-----\n-22== ---------------MDS-----------FAAVATQLGPQF----------AAPS-----\n-23== ----------MERSHLPE-----------TPFDLAHSGPRF----------QAQS-----\n-24== ----------MERSLLPE-----------PPLAMALLGPRF----------EAQT-----\n-25== --------------------------------MIAVSGPSY----------EAFS-----\n-26== ----------------------------------MANQLSY----------SSLG-----\n-27== ---------------------------------------MV----------ESTT-----\n-28== ----------------------------------------M----------GRDL-----\n-29== ---------MMDVNSSGRPDLYGHLRSF-LLPEVGRGLPDL----------SPDGGADPV\n+9== ----------------------------------------MAQQWSLQRLAGRHPQDSYE\n+10== ----------------------------------------MAQQWSLQRLAGRHPQDSYE\n+11== ----------------------------------------MTEAWNVAVFAARRSRDD-D\n+12== ----------------------------------------MAA-WEAAFAARRRHEE--E\n+13== ----------------------------------------MS-----------------S\n+14== ----------MESGNVSS------------SLFGNVST-ALRP----------------E\n+15== ----------MEYHNVSS------------VL-GNVSS-VLRP----------------D\n+16== ----------ME------------------PL-CNASEPPLRP----------------E\n+17== ----------MD------------------AL-CNASEPPLRP----------------E\n+18== --------------------------------MTNATGPQMAY----------------Y\n+19== --------------------------------MANVTGPQMAF----------------Y\n+20== ----------ME----SF------------AVAAAQLGPHFAP----------------L\n+21== ----------ME----SF------------AVAAAQLGPHFAP----------------L\n+22== ----------MD----SF------------AA'..b'-------------\n 33=p ------------------------------------------------------------\n 34== ------------------------------------------------------------\n 35=p ------------------------------------------------------------\n-36== -----------------------------------PQ-----------------------\n+36== ------A---------------PQ------------------------------------\n \n \n-1== --\n-2== --\n-3== --\n-4=p --\n-5=p --\n-6== --\n-7== --\n-8=opsin, --\n-9== --\n-10== --\n-11== --\n-12== --\n-13== --\n-14== --\n-15== --\n-16== --\n-17== --\n-18== --\n-19== --\n-20== --\n-21== --\n-22== --\n-23== --\n-24== --\n-25== --\n-26== --\n-27== QA\n-28== QA\n-29== --\n-30== --\n-31=p --\n-32== --\n-33=p --\n-34== --\n-35=p --\n-36== --\n- \n+1== ---------------------------------------------------------\n+2== ---------------------------------------------------------\n+3== ---------------------------------------------------------\n+4=p ---------------------------------------------------------\n+5=p ---------------------------------------------------------\n+6== ---------------------------------------------------------\n+7== ---------------------------------------------------------\n+8=opsin, ---------------------------------------------------------\n+9== ---------------------------------------------------------\n+10== ---------------------------------------------------------\n+11== ---------------------------------------------------------\n+12== ---------------------------------------------------------\n+13== ---------------------------------------------------------\n+14== ---------------------------------------------------------\n+15== ---------------------------------------------------------\n+16== ---------------------------------------------------------\n+17== ---------------------------------------------------------\n+18== ---------------------------------------------------------\n+19== ---------------------------------------------------------\n+20== ---------------------------------------------------------\n+21== ---------------------------------------------------------\n+22== ---------------------------------------------------------\n+23== ---------------------------------------------------------\n+24== ---------------------------------------------------------\n+25== ---------------------------------------------------------\n+26== ---------------------------------------------------------\n+27== QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA\n+28== QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA\n+29== --------------------------------------------CRKKGHDS-----\n+30== --------------------------------------------CGKKGHDT-----\n+31=p --------------------------------------------CGKKGHDT-----\n+32== ---------------------------------------------------------\n+33=p ---------------------------------------------------------\n+34== ---------------------------------------------------------\n+35=p ---------------------------------------------------------\n+36== ---------------------------------------------------------\n+ \n' |