| Previous changeset 14:6f28e90db932 (2023-10-31) Next changeset 16:8e649f27aa0d (2024-08-22) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 2f6456c314c010fd73f5eeaf809a9afce47353af |
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modified:
macros.xml mafft-add.xml mafft.xml |
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added:
test-data/mafft_auto_linsi.aln test-data/mafft_custom_original.clustal.aln test-data/mafft_custom_parttree.aln test-data/mafft_default.aln test-data/mafft_explicit_amino_blosum80.clustal.aln test-data/mafft_kimura40.phylip.aln test-data/sample_amino.fa test-data/sample_nuc.fa |
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removed:
test-data/mafft_custom_result.aln test-data/mafft_fftns_result.aln test-data/mafft_nwns_result.aln test-data/sample.fa |
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| diff -r 6f28e90db932 -r bf28a8cff401 macros.xml --- a/macros.xml Tue Oct 31 15:48:53 2023 +0000 +++ b/macros.xml Wed Mar 20 07:34:52 2024 +0000 |
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| @@ -1,22 +1,55 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">7.508</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">7.520</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> + <!-- currently, the fasta3 executable is named according to its major version + => needs updating together with the package requirement! --> + <token name="@FASTA3_EXEC@">fasta36</token> <xml name="biotools"> <xrefs> <xref type="bio.tools">MAFFT</xref> </xrefs> </xml> <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">mafft</requirement> - <requirement type="package" version="36.3.8">fasta3</requirement> - </requirements> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mafft</requirement> + <requirement type="package" version="36.3.8">fasta3</requirement> + </requirements> + </xml> + <xml name="weighti_param"> + <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/> + </xml> + <xml name="parttree_parameters"> + <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/> + <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/> + <param argument="--groupsize" type="integer" value="-1" min="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/> + </xml> + <xml name="misc_scoring_scheme"> + <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" /> + <conditional name="gap_costs"> + <param name="use_defaults" type="select" label="Configure gap costs"> + <option value="yes">Use default values</option> + <option value="no">Set values</option> + </param> + <when value="yes"/> + <when value="no"> + <param argument="--ep" type="float" value="0.0" label="Gap extension penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment."/> + <param argument="--op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value"/> + </when> + </conditional> + </xml> + <xml name="global_align_options"> + <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true"> + <param argument="--unalignlevel" type="float" min="0" max="0.8" value="0" label="Over-alignment correction factor" help="The higher this factor the more likely will unrelated sequence stretches in globally related sequences be left unaligned. The default of 0 turns over-alignment correction off, turning it on increases run time."/> + <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/> + </section> </xml> <xml name="citations"> - <citations> - <citation type="doi">10.1093/molbev/mst010</citation> - </citations> + <citations> + <citation type="doi">10.1093/nar/gkf436</citation> + <citation type="doi">10.1093/nar/gki198</citation> + <citation type="doi">10.1093/molbev/mst010</citation> + </citations> </xml> </macros> |
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| diff -r 6f28e90db932 -r bf28a8cff401 mafft-add.xml --- a/mafft-add.xml Tue Oct 31 15:48:53 2023 +0000 +++ b/mafft-add.xml Wed Mar 20 07:34:52 2024 +0000 |
| [ |
| @@ -16,43 +16,53 @@ </version_command> <command> <![CDATA[ + sh mk_symlinks.sh && mafft #if $sequences.sequenceType == 'singleseq' - $sequences.preservegap '$inputSequences' + $sequences.preservegap input_dir/sequence #elif $sequences.sequenceType == 'frags' - --addfragments '$inputSequences' + --addfragments input_dir/sequence #elif $sequences.sequenceType == 'group' - --addprofile '$inputSequences' + --addprofile input_dir/sequence #end if - $keeplength $map $reorder - '$inputAlignment' - > '$outputAlignment' - #if $map == '--mapout' - && mv '${inputSequences}.map' '$outputmap' + $keeplength + $mapout + $reorder + input_dir/alignment > '$outputAlignment' + + #if $mapout + && mv input_dir/sequence.map '$outputmap' #end if ]]> </command> + <configfiles> + <configfile filename="mk_symlinks.sh"><![CDATA[ +mkdir input_dir && +ln -s '$inputSequences' input_dir/sequence && +ln -s '$inputAlignment' input_dir/alignment + ]]></configfile> + </configfiles> <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" > + <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 name="preservegap" type="select" label="Preserve the original alignment." help="Keep the given alignment unchanged .If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved."> + <option value="--add" selected="true" >Yes (--add)</option> + <option value="--seed">No (--seed)</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)" /> + <param argument="--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 argument="--mapout" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of position." 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 argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences." /> </inputs> <outputs> <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/> @@ -63,11 +73,11 @@ <tests> <test expect_num_outputs="1" > <param name="inputSequences" value="add_seq.fa"/> - <param name="inputAlignment" value="mafft_fftns_result.aln"/> + <param name="inputAlignment" value="mafft_default.aln"/> <param name="sequenceType" value="singleseq"/> <param name="preservegap" value="--add"/> <param name="keeplength" value="--keeplength"/> - <param name="map" value=""/> + <param name="mapout" value=""/> <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/> </test> </tests> |
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| diff -r 6f28e90db932 -r bf28a8cff401 mafft.xml --- a/mafft.xml Tue Oct 31 15:48:53 2023 +0000 +++ b/mafft.xml Wed Mar 20 07:34:52 2024 +0000 |
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| b'@@ -1,305 +1,542 @@\n-<?xml version="1.0" encoding="UTF-8"?>\r\n-<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\r\n-<description>Multiple alignment program for amino acid or nucleotide sequences</description>\r\n- <macros>\r\n- <import>macros.xml</import>\r\n- </macros>\r\n- <expand macro="biotools"/>\r\n- <expand macro="requirements" />\r\n- <stdio>\r\n- <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />\r\n- <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />\r\n- </stdio>\r\n- <version_command> <![CDATA[\r\n- mafft --version\r\n- ]]>\r\n- </version_command>\r\n- <command>\r\n- <![CDATA[\r\n-\r\n- #if $cond_flavour.flavourType == \'custom\'\r\n- #if $cond_flavour.dist_flavour.distance_method == \'--fastapair\'\r\n- export FASTA_4_MAFFT=`which fasta36`;\r\n- #end if\r\n- #end if\r\n-\r\n- #if $cond_flavour.flavourType != \'custom\'\r\n- $cond_flavour.flavourType\r\n- #elif $cond_flavour.flavourType == \'custom\'\r\n- ### full parameter options\r\n- mafft\r\n- $cond_flavour.dist_flavour.distance_method\r\n- #if $cond_flavour.dist_flavour.distance_method == \'--6merpair\'\r\n- --retree $cond_flavour.dist_flavour.retree\r\n- $cond_flavour.dist_flavour.distance_method.usetree.parttree\r\n-\r\n- #if $cond_flavour.dist_flavour.distance_method.usetree.parttree==--parttree\r\n- $cond_flavour.dist_flavour.distance_method.usetree.treedistance\r\n- $cond_flavour.dist_flavour.distance_method.usetree.partsize\r\n- $cond_flavour.dist_flavour.distance_method.usetree.groupsize\r\n- #end if\r\n-\r\n- #elif $cond_flavour.dist_flavour.distance_method == \'--globalpair\'\r\n- --weighti $cond_flavour.dist_flavour.weighti\r\n- #elif $cond_flavour.dist_flavour.distance_method == \'--localpair\'\r\n- --weighti $cond_flavour.dist_flavour.weighti\r\n- --lop $cond_flavour.dist_flavour.lop\r\n- --lep $cond_flavour.dist_flavour.lep\r\n- --lexp $cond_flavour.dist_flavour.lexp\r\n- #elif $cond_flavour.dist_flavour.distance_method == \'--genafpair\'\r\n- --weighti $cond_flavour.dist_flavour.weighti\r\n- --lop $cond_flavour.dist_flavour.lop\r\n- --lep $cond_flavour.dist_flavour.lep\r\n- --lexp $cond_flavour.dist_flavour.lexp\r\n- --LOP $cond_flavour.dist_flavour.skipLOP\r\n- --EXP $cond_flavour.dist_flavour.skipEXP 1\r\n- #elif $cond_flavour.dist_flavour.distance_method == \'--fastapair\'\r\n- --weighti $cond_flavour.dist_flavour.weighti\r\n- #end if\r\n- --maxiterate $cond_flavour.iterations\r\n- $cond_flavour.fft\r\n- $cond_flavour.score\r\n- #end if\r\n-\r\n- ## specify threads to use\r\n- --thread \\${GALAXY_SLOTS:-1}\r\n- $datatype\r\n- --ep $ep\r\n- --op $op\r\n-\r\n- #if $matrix_condition.matrix == "BLOSUM"\r\n- --bl $matrix_condition.BLOSUM\r\n- #elif $matrix_condition.matrix == "PAM"\r\n- --jtt $matrix_condition.PAM\r\n- --tm $matrix_condition.tm\r\n- #elif $matrix_condition.matrix == "custom"\r\n- --aamatrix \'$matrix_condition.matrixfile\'\r\n- --fmodel $matrix_condition.fmodel\r\n- #end if\r\n-\r\n- $reorder\r\n- $getTree\r\n- $outputFormat\r\n- \'$inputSequences\' > \'$outputAlignment\';\r\n-\r\n- #if $getTree == "--treeout"\r\n- mv \'${inputSequences}.tree\' \'$outputTree\';\r\n- #end if\r\n- ]]>\r\n- </command>\r\n- <inputs>\r\n- <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>\r\n- <param name="datatype" type="select" label="Data type">\r\n- <option value="">Auto detection</option>\r\n- <option value="--nuc">Nucleic acids</option>\r\n- <option value="--amino">Amino acids</option>\r\n- </param>\r\n- <conditional name="cond_fl'..b' </conditional>\n+ </conditional>\n+ </conditional>\n+ <output name="outputAlignment" ftype="fasta" file="mafft_custom_parttree.aln" />\n+ </test>\n+ <!-- test concatenation of multiple inputs -->\n+ <test expect_num_outputs="2">\n+ <conditional name="input">\n+ <param name="mapping" value="merge"/>\n+ <repeat name="batches">\n+ <param name="inputs" value="sample_amino.fa"/>\n+ </repeat>\n+ <repeat name="batches">\n+ <param name="inputs" value="sample_nuc.fa"/>\n+ </repeat>\n+ </conditional>\n+ <param name="treeout" value="true"/>\n+ <output name="outputAlignment" ftype="fasta">\n+ <metadata name="sequences" value="39"/>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+MAFFT is a multiple sequence alignment (MSA) program, which offers a range of multiple alignment methods.\n+\n+Input types and alignment scoring matrices\n+------------------------------------------\n+\n+For the alignment of *protein* sequences, you can choose between:\n+\n+- different flavors of BLOSUM matrices (`Henikoff S and Henikoff JG, 1992 <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC50453/>`__)\n+- JTT matrices with any point accepted mutation (PAM) rate (`Jones, Taylor and Thornton, 1992 <https://pubmed.ncbi.nlm.nih.gov/1633570/>`__)\n+- PAM-based matrices optimized for transmembrane proteins (`Jones, Taylor and Thornton, 1994 <https://pubmed.ncbi.nlm.nih.gov/8112466/>`__)\n+\n+For nucleic acid sequence alignment, MAFFT uses Kimura\'s two parameter model (`Kimura 1980 <https://pubmed.ncbi.nlm.nih.gov/7463489/>`__)\n+with a transitions to transversions ratio of 2 (kappa 2), but lets you configure the PAM value.\n+\n+The tool can also try to autodetect the sequence type from the input(s).\n+In this mode, it will use the BLOSUM 62 matrix if it detects amino acids input, and the Kimura kappa 2 PAM200 matrix for nucleic acids.\n+\n+\n+Pre-configured MSA methods\n+--------------------------\n+\n+From the `MAFFT man page <https://mafft.cbrc.jp/alignment/software/manual/manual.html>`__, an overview of the different predefined flavours of the tool.\n+\n+**Accuracy-oriented methods:**\n+\n+- *L-INS-i* (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):\n+\n+ - mafft --localpair --maxiterate 1000 input [> output]\n+- *G-INS-i* (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):\n+\n+ - mafft --globalpair --maxiterate 1000 input [> output]\n+- *E-INS-i* (suitable for sequences containing large unalignable regions; recommended for <200 sequences):\n+\n+ - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.\n+\n+**Speed-oriented methods:**\n+\n+- *FFT-NS-i* (iterative refinement method; two cycles only):\n+\n+ - mafft --retree 2 --maxiterate 2 input [> output]\n+- *FFT-NS-2* (fast; progressive method):\n+\n+ - mafft --retree 2 --maxiterate 0 input [> output]\n+- *NW-NS-i* (iterative refinement method without FFT approximation; two cycles only):\n+\n+ - mafft --retree 2 --maxiterate 2 --nofft input [> output]\n+- *NW-NS-2* (fast; progressive method without the FFT approximation):\n+\n+ - mafft --retree 2 --maxiterate 0 --nofft input [> output]\n+- *NW-NS-PartTree-1* (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):\n+\n+ - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]\n+- *FFT-NS-1* (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):\n+\n+ - mafft --retree 1 --maxiterate 0 input [> output]\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_auto_linsi.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_auto_linsi.aln Wed Mar 20 07:34:52 2024 +0000 |
| [ |
| b"@@ -0,0 +1,504 @@\n+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n+M------------------NGTE-G------DNFYVPF----SNKTGLARSPYEYPQY--\n+--------------------------------------------------YLAEPW----\n+---------------KYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLA\n+MANLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERY\n+IVICKPMGNF-RFGNTHAIMGVAFTWIMALAC-AAPPLVG-WS-----RYIPEGMQCSCG\n+PDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQESA-------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------------------------STQKAEKEVTRMVVLMVIGFLVCWVPYAS\n+VAFYIFT---HQGS-DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTL-----\n+CC-----GKNPLGDDE-SGA-STSK-TEVSSVS-TSPVSPA-------------------\n+------------------------------------------------------------\n+---------------\n+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n+M------------------NGTE-G------PNFYVPF----SNITGVVRSPFEQPQY--\n+--------------------------------------------------YLAEPW----\n+---------------QFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA\n+VADLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERY\n+VVVCKPMSNF-RFGENHAIMGVAFTWVMALAC-AAPPLVG-WS-----RYIPEGMQCSCG\n+IDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESA-------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------------------------TTQKAEKEVTRMVIIMVIFFLICWLPYAS\n+VAMYIFT---HQGS-NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSL-----\n+CC-----GKNPLGDDE-ASA-TASK-TETSQVA-PA------------------------\n+------------------------------------------------------------\n+---------------\n+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n+M------------------NGTE-G------INFYVPM----SNKTGVVRSPFEYPQY--\n+--------------------------------------------------YLAEPW----\n+---------------KYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLA\n+VADLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERY\n+IVVCKPMGNF-RFSATHAMMGIAFTWVMAFSC-AAPPLFG-WS-----RYMPEGMQCSCG\n+PDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQESA-------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------------------------TTQKAEKEVTRMVILMVLGFMLAWTPYAV\n+VAFWIFT---NKGA-DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTI-----\n+CC-----GKNPFGDEDVSSTVSQSK-TEVSSVS-SSQVSPA-------------------\n+------------------------------------------------------------\n+---------------\n+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n+M------------------NGTE-G------KNFYVPM----SNRTGLVRSPFEYPQY--\n+--------------------------------------------------YLAEPW----\n+---------------QFKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLA\n+VAGTIMVCFG-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERY\n+IVVCKPMGSF-KFSSSHAFAGIAFTWVMALAC-AAPPLFG-WS-----RYIPEGMQCSCG\n+PDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDSA-------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------------------------STQKAEREVTKMVILMVFGFLIAWTPYAT\n+VAAWIFF---NKGA-DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTI-----\n+FC-----GKNPLGDDE-SSTVSTSK-TEVSSVS-PA------------------------\n+------------------------------------------------------------\n+---------------\n+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n+M------------------NGTE-G------NNFYVPL----SNRTGLVRSPFEYPQY--\n+--------------------------------------------------YLAEPW----\n+---------------QFKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLA\n+VAGAIMVCFG-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERY\n+IVVCKPMGSF-KFSSTHASAGIAFTWVMAMAC-AAPPLVG-WS-----RYIPEGIQCSCG\n+PDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDSA-------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------------------------STQKAEREVTKMVILMVLGFLVAWTPYAT\n+VAAWIFF---NKGA"..b"PF-E---------------TGGNTTGIS\n+----------DVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLA\n+VTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRY\n+WAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTIS\n+KDH----------GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT\n+RHGASPAPQPKK-----SVNGE--SGSRNWRLGVESKAGGALC-----------------\n+-------------------------------ANGAVRQGDDGAALEVIEVHRVGNSKEHL\n+PLPSEAG--PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFI\n+VALVLPF---CESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKII-----\n+KCKFCRQ-----------------------------------------------------\n+------------------------------------------------------------\n+---------------\n+> 33=p A35181 serotonin receptor class 1A - rat\n+M------------------DVFSFG-------------------------------QG--\n+------------------------NNTTASQEPF-G---------------TGGNVTSIS\n+----------DVTFSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLA\n+VTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRY\n+WAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTIS\n+KDH----------GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT\n+SLGTSSAPPPKK-----SLNGQ--PGSGDWRRCAENRAVGTPC-----------------\n+-------------------------------TNGAVRQGDDEATLEVIEVHRVGNSKEHL\n+PLPSESG--SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFI\n+VALVLPF---CESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKII-----\n+KCKFCRR-----------------------------------------------------\n+------------------------------------------------------------\n+---------------\n+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\n+M------------------ANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLV\n+TSDFNDSYGLTGQFINGSHSSRSRDNASANDT--------------SATNMTDDRYWSLT\n+----------VYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLA\n+VADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRY\n+WAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIIS\n+QDK----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKT\n+EETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPEN\n+ANGVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAML-ERQCNNGKK--\n+-----------------ISSNDTPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFI\n+IALIGPF---VDPE-GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----\n+FGKYRRGHR---------------------------------------------------\n+------------------------------------------------------------\n+---------------\n+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n+M------------------ANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLV\n+TSDFNDSYGLTGQFINGSHSSRSRDNASANDT--------------SATNMTDDRYWSLT\n+----------VYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLA\n+VADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRY\n+WAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIIS\n+QDK----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKT\n+EETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPEN\n+ANGVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAML-ERQCNNGKK--\n+-----------------ISSNDTPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFI\n+IALIGPF---VDPE-GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----\n+FGKYRRGHR---------------------------------------------------\n+------------------------------------------------------------\n+---------------\n+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n+M------------------EGAE-GQEELDWEALYLRLPL--------------------\n+------------------------QNCSWNSTGWEPNW--------NVTVVPNTTWWQAS\n+-----APFDTPAALVRAAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLA\n+VADLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRY\n+WAVTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVS\n+QDV----------GYQIFATASSFYVPVLIILILYWRIYQTARKRIRRRRGATARGGVGP\n+-------PP-----------------------------------------------VPAG\n+GALVAGGGSGGIAAAVVAVIGRPLPTISETTTTGFTNVSSNNTSPE---KQSCANGLEAD\n+PPTTGYGAVAAAYYPSLVRRK------PKEAADSKRERKAAKTLAIITGAFVACWLPFFV\n+LAILVPT---CDCE--VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLL-----\n+CGRRVRRRRA-----------------------------PQ-------------------\n+------------------------------------------------------------\n+---------------\n" |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_custom_original.clustal.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_custom_original.clustal.aln Wed Mar 20 07:34:52 2024 +0000 |
| b |
| b'@@ -0,0 +1,496 @@\n+CLUSTAL format alignment by MAFFT G-INS-i (v7.520)\n+\n+\n+1== MN----------------------------------------------------------\n+2== MN----------------------------------------------------------\n+3== MN----------------------------------------------------------\n+4=p MN----------------------------------------------------------\n+5=p MN----------------------------------------------------------\n+6== MK----------------------------------------------------------\n+7== MR----------------------------------------------------------\n+8=opsin, ------------------------------------------------------------\n+9== MA------QQWS-LQRLAGRHPQDS--------------------------YED------\n+10== MA------QQWS-LQRLAGRHPQDS--------------------------YED------\n+11== MT------EAWNVAVFAARRSRDD----------------------------DD------\n+12== MA-------AWE-AAFAARRRHEE----------------------------ED------\n+13== MS----------------------------------------------------------\n+14== MESGNVS-----------------------------------------------------\n+15== MEYHNVS-----------------------------------------------------\n+16== ME----------------------------------------------------------\n+17== MD----------------------------------------------------------\n+18== MT----------------------------------------------------------\n+19== MA----------------------------------------------------------\n+20== MESF--------------------------------------------------------\n+21== MESF--------------------------------------------------------\n+22== MDSF--------------------------------------------------------\n+23== MERSHLP---------------------------------------------------ET\n+24== MERSLLP---------------------------------------------------EP\n+25== MI----------------------------------------------------------\n+26== M-----------------------------------------------------------\n+27== MV----------------------------------------------------------\n+28== MG----------------------------------------------------------\n+29== MMDVN-----------SSGRPDLYGHLRSFLLPEVGRGLPDLSPDG------------GA\n+30== M-----------------------------------------------------------\n+31=p M-----------------------------------------------------------\n+32== MDVLS-------------------------------------------------------\n+33=p MDVFS-------------------------------------------------------\n+34== MANFTFGDLALD-VARMGGLASTPSGLRS-----TGLTTPGLSPTGLVTSDFNDSYGLTG\n+35=p MANFTFGDLALD-VARMGGLASTPSGLRS-----TGLTTPGLSPTGLVTSDFNDSYGLTG\n+36== ME----------------------------------------------------------\n+ \n+\n+1== ----GTEG--DNFY------------VPFSNKTG----------------------LARS\n+2== ----GTEG--PNFY------------VPFSNITG----------------------VVRS\n+3== ----GTEG--INFY------------VPMSNKTG----------------------VVRS\n+4=p ----GTEG--KNFY------------VPMSNRTG----------------------LVRS\n+5=p ----GTEG--NNFY------------VPLSNRTG----------------------LVRS\n+6== ----QVPEFHEDFY------IPIP--LDINNLSA------------------------YS\n+7== ----KMSE--EEFY------------L-FKNISS----------------------V--G\n+8=opsin, ------------------------------------------------------------\n+9== ----STQS--SIFT------------YTNSNSTR-------------------------G\n+10== ----STQS--SIFT------------YTNSNSTR-------------------------G\n+11== ----TTRG--SVFT------------YTNTNNTR-------------------------G\n+12== ----TTRD--SVFT------------YTNSNNTR-------------------------G\n+13== ----SNSS------------------QAPPNGTP-------------------------G\n+14== SSLFGN'..b'\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== ---------------------------------------MP-------------------\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== YQP---PPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGA\n+28== YPPQGYAPPPQGYPPQGYPPQGY--PPQGYPPQGYPP---PPQGAPPQGAPP------AA\n+29== ------------------------------------------------------------\n+30== ------------------------------------------------------------\n+31=p ------------------------------------------------------------\n+32== ------------------------------------------------------------\n+33=p ------------------------------------------------------------\n+34== ------------------------------------------------------------\n+35=p ------------------------------------------------------------\n+36== ------------------------------------------------------------\n+ \n+\n+1== ---------SPA\n+2== ---------APA\n+3== ---------SPA\n+4=p ---------SPA\n+5=p ---------SPA\n+6== ------------\n+7== ---------GPN\n+8=opsin, ------------\n+9== ---------SPA\n+10== ---------SPA\n+11== ---------APA\n+12== ---------SPA\n+13== --------AHPV\n+14== ---------TAA\n+15== ---------TAA\n+16== ---------TAA\n+17== ---------SAA\n+18== ---------DKA\n+19== ---------EKS\n+20== ---------SKA\n+21== ---------SKA\n+22== ---------SKA\n+23== ---------SKA\n+24== ---------SKD\n+25== ---------SNA\n+26== --------IPEA\n+27== PPQGVDNQAYQA\n+28== PPQGVDNQAYQA\n+29== ---------HDS\n+30== ---------HDT\n+31=p ---------HDT\n+32== -----------Q\n+33=p -----------R\n+34== ---------GHR\n+35=p ---------GHR\n+36== ---------APQ\n+ \n' |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_custom_parttree.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_custom_parttree.aln Wed Mar 20 07:34:52 2024 +0000 |
| [ |
| b"@@ -0,0 +1,504 @@\n+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n+MN-------------------GTE------GDNFYVPF----------------SNKTGL\n+-----------ARSPYEYPQY-----YLAEPWK--------------------Y------\n+------------------SALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNL\n+AMANLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIER\n+YIVICKPMGN-FRFGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSC\n+GPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE-----------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---AAAAQQ------------------------------------ESASTQKAEKEVTRM\n+VVLMVIGFLVCWVPYASVAFYIFT-HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMN\n+KQFRNCMITTLC----C---GKNPLGD-DE--SGASTSKTEV------------------\n+------------------------------------------------------------\n+---SSVS-------TSPVSP-A----------\n+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n+MN-------------------GTE------GPNFYVPF----------------SNITGV\n+-----------VRSPFEQPQY-----YLAEPWQ--------------------F------\n+------------------SMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNL\n+AVADLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIER\n+YVVVCKPMSN-FRFGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSC\n+GIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE-----------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---AAAQQQ------------------------------------ESATTQKAEKEVTRM\n+VIIMVIFFLICWLPYASVAMYIFT-HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMN\n+KQFRNCMLTSLC----C---GKNPLGD-DE--ASATASKTE-------------------\n+------------------------------------------------------------\n+--------------TSQVAP-A----------\n+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n+MN-------------------GTE------GINFYVPM----------------SNKTGV\n+-----------VRSPFEYPQY-----YLAEPWK--------------------Y------\n+------------------RLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNL\n+AVADLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIER\n+YIVVCKPMGN-FRFSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSC\n+GPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE-----------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---AAAQQQ------------------------------------ESATTQKAEKEVTRM\n+VILMVLGFMLAWTPYAVVAFWIFT-NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMN\n+KQFRNCMITTIC----C---GKNPFGD-EDVSSTVSQSKTEV------------------\n+------------------------------------------------------------\n+---SSVS-------SSQVSP-A----------\n+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n+MN-------------------GTE------GKNFYVPM----------------SNRTGL\n+-----------VRSPFEYPQY-----YLAEPWQ--------------------F------\n+------------------KILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNL\n+AVAGTIMVCFG-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIER\n+YIVVCKPMGS-FKFSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSC\n+GPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA-----------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---AAAQQQ------------------------------------DSASTQKAEREVTKM\n+VILMVFGFLIAWTPYATVAAWIFF-NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLN\n+KQFRNCMLTTIF----C---GKNPLGD-DE-SSTVSTSKTEV------------------\n+------------------------------------------------------------\n+---SS------------VSP-A----------\n+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n+MN-------------------GTE------GNNFYVPL----------------SNRTGL\n+-----------VRSPFEYPQY-----YLAEPWQ--------------------F------\n+------------------KLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNL\n+AVAGAIMVCFG-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIER\n+YIVVCKPMGS-FKFSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSC\n+GPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA-----------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---AAAQQ"..b"LIGSL\n+AVTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDR\n+YWAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP--EDRSDPD---AC\n+TIS--------KDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK-----------\n+----------------------------TVKKVEKTGADTRHGASPAPQPKKSVNGESGS\n+RNWRLGVESKAGGAL-CANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAP-\n+----ASFERK-----------NERNA----------------EA-KRKMALARERKTVKT\n+LGIIMGTFILCWLPFFIVALVLPF-CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFN\n+KDFQNAFKKIIK--------CKFCR-----------------------------------\n+------------------------------------------------------------\n+-------------------------------Q\n+> 33=p A35181 serotonin receptor class 1A - rat\n+M-DVFS-------------FGQ--------GNNTTASQEPFGTG----------GNVTSI\n+-------------------------SDVTFSYQ---------------------------\n+------------------VITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSL\n+AVTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDR\n+YWAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP--EDRSDPD---AC\n+TIS--------KDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK-----------\n+----------------------------TVRKVEKKGAGTSLGTSSAPPPKKSLNGQPGS\n+GDWRRCAENRAVGTP-CTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESGSNSYAP-\n+----ACLERK-----------NERNA----------------EA-KRKMALARERKTVKT\n+LGIIMGTFILCWLPFFIVALVLPF-CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFN\n+KDFQNAFKKIIK--------CKFCR-----------------------------------\n+------------------------------------------------------------\n+-------------------------------R\n+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\n+M-ANFT-------------FGDLALDVARMGGLASTPSGLRSTG----------LTTPGL\n+SPTG------------------LVTSDFNDSYGLTGQFINGSHSSRSRDNASAN-DTSAT\n+NMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSL\n+AVADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDR\n+YWAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NN--DPDKTGTC\n+IIS--------QDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLK\n+TEETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK--------\n+--------NRAKKLPENANGVNSNSSSSERLKQIQIE-----------TAEAFANGCAEE\n+AS-IAMLERQ-CNNGKKISSNDTPYS----------------RT-REKLELKRERKAART\n+LAIITGAFLICWLPFFIIALIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFS\n+PEFRSAFQKILF--------GKYRRG----------------------------------\n+------------------------------------------------------------\n+------------------------------HR\n+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n+M-ANFT-------------FGDLALDVARMGGLASTPSGLRSTG----------LTTPGL\n+SPTG------------------LVTSDFNDSYGLTGQFINGSHSSRSRDNASAN-DTSAT\n+NMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSL\n+AVADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDR\n+YWAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NN--DPDKTGTC\n+IIS--------QDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLK\n+TEETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK--------\n+--------NRAKKLPENANGVNSNSSSSERLKQIQIE-----------TAEAFANGCAEE\n+AS-IAMLERQ-CNNGKKISSNDTPYS----------------RT-REKLELKRERKAART\n+LAIITGAFLICWLPFFIIALIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFS\n+PEFRSAFQKILF--------GKYRRG----------------------------------\n+------------------------------------------------------------\n+------------------------------HR\n+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n+M-EG-A-------------EGQEELD----WEALYLRLPLQNCS----------WNSTGW\n+EPNW------------------NVTVVPNTTWW----------------QASAPFDTPAA\n+LVRA--------------AAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSL\n+AVADLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDR\n+YWAVTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDL--RC\n+VVS--------QDVGYQIFATASSFYVPVLIILILYWRIYQTARKRIRR-----------\n+----------------------------------RRGATARGGVGPPPVP----------\n+-----------------AGGALVAGGGSGGIAAAVVAVIGRP---LPTISETTTTGFTNV\n+SSNNTSPEKQSCANGLEA---DPPTTGYGAVAAAYYPSLVRRKP-KEAADSKRERKAAKT\n+LAIITGAFVACWLPFFVLAILVPT-CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFS\n+PEFRHAFQRLLC--------GRRVRRR----R----------------------------\n+------------------------------------------------------------\n+-----------------------------APQ\n" |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_custom_result.aln --- a/test-data/mafft_custom_result.aln Tue Oct 31 15:48:53 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,458 +0,0 @@\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 6f28e90db932 -r bf28a8cff401 test-data/mafft_default.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_default.aln Wed Mar 20 07:34:52 2024 +0000 |
| [ |
| b"@@ -0,0 +1,468 @@\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"'92]\n+----------MDVLSP--------------------------------------------\n+---------------GQGNNTTSPPAPFET-GGNTTGISDVT---------VSYQ--VIT\n+SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV\n+L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA\n+LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST\n+FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------\n+--------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR--\n+-------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG--\n+PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C\n+ESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RQ----\n+------------------------------------------------------------\n+---------------------------------------------------------\n+> 33=p A35181 serotonin receptor class 1A - rat\n+----------MDVFSF--------------------------------------------\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" |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_explicit_amino_blosum80.clustal.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_explicit_amino_blosum80.clustal.aln Wed Mar 20 07:34:52 2024 +0000 |
| b |
| b'@@ -0,0 +1,458 @@\n+CLUSTAL format alignment by MAFFT FFT-NS-2 (v7.520)\n+\n+\n+1== ----------------------------------------MN------------------\n+2== ----------------------------------------MN------------------\n+3== ----------------------------------------MN------------------\n+4=p ----------------------------------------MN------------------\n+5=p ----------------------------------------MN------------------\n+6== ----------------------------------------MK------------------\n+7== ----------------------------------------MR------------------\n+8=opsin, ------------------------------------------------------------\n+9== ----------------------------------------MAQQWSLQRLAGRHPQDS--\n+10== ----------------------------------------MAQQWSLQRLAGRHPQDS--\n+11== ----------------------------------------MTEAWNVAVFAARRSRDD--\n+12== ----------------------------------------MA-AWEAAFAARRRHEE---\n+13== ----------------------------------------MS------------------\n+14== ----------MESGNVS-------------SSLFGNVSTALR------------------\n+15== ----------MEYHNVS-------------SVL-GNVSSVLR------------------\n+16== ----------ME-------------------PLCNASEPPLR------------------\n+17== ----------MD-------------------ALCNASEPPLR------------------\n+18== --------------------------------MTNATGPQMA------------------\n+19== --------------------------------MANVTGPQMA------------------\n+20== ----------ME---SF-------------AVAAAQLGPHFA------------------\n+21== ----------ME---SF-------------AVAAAQLGPHFA------------------\n+22== ----------MD---SF-------------AAVATQLGPQFA------------------\n+23== -----MERSHLP---ET-------------PFDLAHSGPRFQ------------------\n+24== -----MERSLLP---EP-------------PLAMALLGPRFE------------------\n+25== --------------------------------MIAVSGPSYE------------------\n+26== ----------------------------------MANQLSYS------------------\n+27== ---------------------------------------MVE------------------\n+28== ----------------------------------------MG------------------\n+29== ---------MMDVNSSGRPDLYGHLRSFL-LPEVGRGLPDLSPDGGADPVAG-SWAPHLL\n+30== -------------------------------------------------------MPHLL\n+31=p -------------------------------------------------------MPHLL\n+32== ----------MDVLSP--------------------------------------------\n+33=p ----------MDVFSF--------------------------------------------\n+34== MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYG---L\n+35=p MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYG---L\n+36== -MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNVTVVPNTTW-----\n+ \n+\n+1== -----GTE--GDN-FYVP----FSNKTGLARSPYEYPQY-YLAEPWK-----------YS\n+2== -----GTE--GPN-FYVP----FSNITGVVRSPFEQPQY-YLAEPWQ-----------FS\n+3== -----GTE--GIN-FYVP----MSNKTGVVRSPFEYPQY-YLAEPWK-----------YR\n+4=p -----GTE--GKN-FYVP----MSNRTGLVRSPFEYPQY-YLAEPWQ-----------FK\n+5=p -----GTE--GNN-FYVP----LSNRTGLVRSPFEYPQY-YLAEPWQ-----------FK\n+6== -----QVPEFHED-FYIPIPLDINNLSAY--SPFLVPQD-HLGNQGI-----------FM\n+7== -----KMS--EEE-FYL-----FKNISSV--GPWDGPQY-HIAPVWA-----------FY\n+8=opsin, ------------------------------------------------------------\n+9== ----YEDSTQSSI-FT------YTNSNST-RGPFEGPNY-HIAPRWV-----------YH\n+10== ----YEDSTQSSI-FT------YTNSNST-RGPFEGPNY-HIAPRWV-----------YH\n+11== -----DDTTRGSV-FT------YTNTNNT-RGPFEGPNY-HIAPRWV-----------YN\n+12== -----EDTTRDSV-FT------YTNSNNT-RGPFEGPNY-HIAPRWV-----------YN\n+13== -----SNSSQAP-------------PNGT-PGPFDGPQWPYQAPQST-----------YV\n+14== -----'..b'--\n+20== -SSDAQSQA-TASEA-ESKA----------------------------------------\n+21== -SSDAQSQA-TASEA-ESKA----------------------------------------\n+22== -SSEAQSQA-TTSEA-ESKA----------------------------------------\n+23== -PDAPASDTETTSEA-DSKA----------------------------------------\n+24== -PDAPPSDTETTSEA-ESKD----------------------------------------\n+25== -DAVSTTSGTTTVTD-NEKSNA--------------------------------------\n+26== -DVKSEASATTTMEE-KPKIPEA-------------------------------------\n+27== -DAEEEVVASER--G-GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPP\n+28== -DAETEIPAGESSDA-APSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPP\n+29== -NINRKLSAAGMHEALKLAERPERPEFVL--------QNADY------------------\n+30== -NINRKLSAAGMHEALKLAERPERSEFVL--------QNSDH------------------\n+31=p -NINRKLSAAGMHEALKLAERPERSEFVL--------QNSDH------------------\n+32== -RQ---------------------------------------------------------\n+33=p -RR---------------------------------------------------------\n+34== -RGHR-------------------------------------------------------\n+35=p -RGHR-------------------------------------------------------\n+36== -RRRRA---------------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== QGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA\n+28== QGY--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' |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_fftns_result.aln --- a/test-data/mafft_fftns_result.aln Tue Oct 31 15:48:53 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,468 +0,0 @@\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"'92]\n-----------MDVLSP--------------------------------------------\n----------------GQGNNTTSPPAPFET-GGNTTGISDVT---------VSYQ--VIT\n-SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV\n-L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA\n-LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST\n-FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------\n---------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR--\n--------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG--\n-PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C\n-ESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RQ----\n-------------------------------------------------------------\n----------------------------------------------------------\n-> 33=p A35181 serotonin receptor class 1A - rat\n-----------MDVFSF--------------------------------------------\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" |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_kimura40.phylip.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_kimura40.phylip.aln Wed Mar 20 07:34:52 2024 +0000 |
| b |
| @@ -0,0 +1,77 @@ + 3 948 +MZ681498.1 atgcatgtat aagtataacc tgccagacag ggaaactgcg gacggctcat +MZ681497.1 ---------- ---------- ---------- -----ctgcg gacggctcat +ON855043.1 ---------- ---------- -ggccgtca- -----ctccg gggggacaac + + tacaacagcc ttaatttact tgaccttgac aacctacttg gataactgcg + tacaacagcc ttaatttact tgaccttgac aacctacttg gataactgcg + acaaacgccc tgagggcttt actcgttggg gtgcaaactg ga-------- + + gtaattctgg agctaataca tgcaccaaag ctccgatccc tcgtggagag + gtaattctgg agctaataca tgcaccaaag ctccgatccc tcgtggagag + ---------- ---------- ---------- ---------- ---tcgagtg + + gagcgcattt gttcgccaca aaaccaaacg ccccacaagg gcgttcagtg + gagcgcattt gttcgccaca aaaccaaacg ccccacaagg gcgttcagtg + gcgcacacat cccttccacg caa--agacc tgctgaagag gtcggaggcg + + ttgactcaga ataact---- ---------- -------aag ctgatcgcac + ttgactcaga ataact---- ---------- -------aag ctgatcgcac + atgagtccga gcaaccccac aagcaaccag gttggggaag ctg--cacac + + ggtctt---- ---------- ----gcaccg gcgacgtgtc tttcaagtgt + ggtctt---- ---------- ----gcaccg gcgacgtgtc tttcaagtgt + gatactggga tgcacgcccc cagggcacct aacggctgcc gctggcgtct + + ctgccttatc aactttcgat ggtagtgtat ctgcctacca tggttgtgac + ctgccttatc aactttcgat ggtagtgtat ctgcctacca tggttgtgac + gtgcgtcgtt ga---gcagt tgttgcgcac ttgctt---- ttgtcggagc + + gggtaacgga ggataagggt tcgactccgg agaaggggcc tgagaaatgg + gggtaacgga ggataagggt tcgactccgg agaaggggcc tgagaaatgg + tgtactcgga gcatgctggc atggacccac acaaaag--- ---------- + + ccactacgtc taaggatggc agcaggcgcg caaattaccc actctcaaca + ccactacgtc taaggatggc agcaggcgcg caaattaccc actctcaaca + ---------- --tgtgtggc agcggccaca ca------cc cctgtccatg + + cgctgaggag gtagtgaaga gaaataacga gaccgttctc acatgaggcc + cgctgaggag gtagtgaaga gaaataacga gaccgttctc acatgaggcc + tcctacgga- ---------- -ccgtagcta gggcgtgct- ---------- + + ggtcatcgga atgggtacaa cttaaaccct ttaacgagta tctatgagag + ggtcatcgga atgggtacaa cttaaaccct ttaacgagta tctatgagag + ---------- ---------- ---------- ---------- ---------- + + ggcaagtctg gtgccagcag ccgcggtaat tccagctctc aaaatgcata + ggcaagtctg gtgccagcag ccgcggtaat tccagctctc aaaatgcata + ---------- ---------- -ctgggtttc ttcggctggc agtgttgcta + + gaattattgc tgcggttaaa aagctcgtag ttggatctgt gctggccgcc + gaattattgc tgcggttaaa aagctcgtag ttggatctgt gctggccgcc + cgtccgtggc tgtgatgaga cgacgcg--- ---------- ---------- + + cggtctgctc gctgagcacg cactggtgcg gtcggctttc ctgcccggta + cggtctgctc gctgagcacg cactggtgcg gtcggctttc ctgcccggta + ---------- -----gtagg gccttgtgcg atgcgcct-- ---------- + + cctccccggc gttggccttc accggtcggc gtcggtggcc gggcgagttt + cctccccggc gttggccttc accggtcggc gtcggtggcc gggcgagttt + --------gc acttggctta a--------- ------gact tgatgagctc + + actttgaaca aatcagag-- -----tgctt caaacaggcg tttcgcttga + actttgaaca aatcagag-- -----tgctt caaacaggcg tttcgcttga + actgcgaaga gccgccagca accttttttt catatacatt ttttacaggc + + atgttcgtgc atggaataat agaagaggat ttcggtccga ttttgttggt + atgttcgtgc atggaataat agaagaggat ttcggtccga ttttgttggt + acacttgtgt gctgatgaac aaaa------ ---------- ---------- + + tttgctgacc gagataatgg ttaacagaga caaacggggc cattcgtatt + tttgctgacc gagataatgg ttaacagaga caaacggggc cattcgtatt + ---------- ---------- ---------- ---------- -------att + + gctacgtgag aggtg----- ---------- ---------- -------- + gctacgtgag aggtgaaatt cttggaccgt agcaagacgg actacagc + ctagccttat cggtggatca ctcggctcgt aggtcgatg- -------- + |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/mafft_nwns_result.aln --- a/test-data/mafft_nwns_result.aln Tue Oct 31 15:48:53 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,458 +0,0 @@\n-CLUSTAL format alignment by MAFFT NW-NS-2 (v7.455)\n-\n-\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== ----------------------------------------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------------AAVATQLGPQFAA----------------P\n-23== -----MERSHLP----ET------------PFDLAHSGPRFQA----------------Q\n-24== -----MERSLLP----EP------------PLAMALLGPRFEA----------------Q\n-25== --------------------------------MIAVSGPSYEA----------------F\n-26== ----------------------------------MANQLSYSS----------------L\n-27== ---------------------------------------MVES----------------T\n-28== ----------------------------------------MGR----------------D\n-29== ---------MMDVNSSGRPDLYGHLRSFL-LPEVGRGLPDLSPDGGA------------D\n-30== ------------------------------------------------------------\n-31=p ------------------------------------------------------------\n-32== ----------MDVLSP--------------------------------------------\n-33=p ----------MDVFSF--------------------------------------------\n-34== MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T\n-35=p MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T\n-36== -MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNV------------T\n- \n-\n-1== E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL\n-2== E--G--PNFYVP----FSNITGVVRSPFEQPQY-------YLAEPWQ---------FSML\n-3== E--G--INFYVP----MSNKTGVVRSPFEYPQY-------YLAEPWK---------YRLV\n-4=p E--G--KNFYVP----MSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKIL\n-5=p E--G--NNFYVP----LSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKLL\n-6== PEFH--EDFYIPIPLDINNLS--AYSPFLVPQD-------HLGNQGI---------FMAM\n-7== S--E--EEFYL-----FKNIS--SVGPWDGPQY-------HIAPVWA---------FYLQ\n-8=opsin, ------------------------------------------------------------\n-9== DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT\n-10== DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT\n-11== DTTR--GSVFT-----YTNTNN-TRGPFEGPNY-------HIAPRWV---------YNLV\n-12== DTTR--DSVFT-----YTNSNN-TRGPFEGPNY-------HIAPRWV---------YNLT\n-13== NSSQ--AP-----------PNG-TPGPFDGPQW------PYQAPQST---------YVGV\n-14== ARLS--'..b'AQSQA-TTSEA-ESKA-----------------------------------\n-23== DEPK--PDAPASDTETTSEA-DSKA-----------------------------------\n-24== DEPK--PDAPPSDTETTSEA-ESKD-----------------------------------\n-25== EPSS--DAVSTTSGTTTVTD-NEKSNA---------------------------------\n-26== ESGS--DVKSEASATTTMEE-KPKIPEA--------------------------------\n-27== EDAN--DAEEEVVASER--G-GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP\n-28== EDDK--DAETEIPAGESSDA-APSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP\n-29== ------KLSAAGMHEALKLAERPERPEF------------VLQNADY-------------\n-30== ------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------\n-31=p ------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------\n-32== ------------------------------------------------------------\n-33=p ------------------------------------------------------------\n-34== ------------------------------------------------------------\n-35=p ------------------------------------------------------------\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== 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' |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/sample.fa --- a/test-data/sample.fa Tue Oct 31 15:48:53 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,285 +0,0 @@\n-> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n-MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF\n-VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG\n-GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP\n-EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES\n-ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL\n-YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA\n-> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n-MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\n-VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\n-GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP\n-EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES\n-ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI\n-YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA\n-> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n-MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL\n-VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG\n-GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP\n-EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES\n-ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL\n-YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA\n-> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n-MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV\n-VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG\n-GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP\n-EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS\n-ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL\n-YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA\n-> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n-MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI\n-CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG\n-GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP\n-EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS\n-ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL\n-YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA\n-> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-\n-MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI\n-LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL\n-ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS\n-RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA\n-QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK\n-ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK\n-> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]\n-MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL\n-RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV\n-TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL\n-QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT\n-QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP\n-IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN\n-> 8=opsin, greensensitive human (fragment) S07060\n-DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP\n-FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS\n-YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC\n-> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]\n-MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM\n-IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV\n-LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA\n-AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL\n-QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH\n-PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS\n-VSPA\n-> 10== Z68193 1 human Red Opsin <>[]\n-MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM\n-IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV\n-LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS\n-AVWTAPPIFGWSRYWPH"..b"ISIDR\n-YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT\n-IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE\n-ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC\n-IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK\n-LAERPERPEFVLQNADYCRKKGHDS\n-> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]\n-MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL\n-VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM\n-DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW\n-AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV\n-QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL\n-PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC\n-QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT\n-> 31=p A47425 serotonin receptor 5HT-7 - rat\n-MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL\n-VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM\n-DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW\n-AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV\n-QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL\n-PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC\n-QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT\n-> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]\n-MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA\n-IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC\n-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED\n-RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT\n-RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN\n-SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP\n-FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC\n-RQ\n-> 33=p A35181 serotonin receptor class 1A - rat\n-MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA\n-IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC\n-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED\n-RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT\n-SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN\n-SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP\n-FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC\n-RR\n-> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\n-MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS\n-HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV\n-MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT\n-ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP\n-DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE\n-ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA\n-NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK\n-LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL\n-NPIIYTIFSPEFRSAFQKILFGKYRRGHR\n-> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n-MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS\n-HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV\n-MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT\n-ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP\n-DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE\n-ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA\n-NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK\n-LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL\n-NPIIYTIFSPEFRSAFQKILFGKYRRGHR\n-> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n-MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR\n-AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV\n-YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM\n-IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI\n-LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI\n-SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR\n-ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT\n-VFSPEFRHAFQRLLCGRRVRRRRAPQ\n" |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/sample_amino.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_amino.fa Wed Mar 20 07:34:52 2024 +0000 |
| [ |
| b"@@ -0,0 +1,285 @@\n+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF\n+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG\n+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP\n+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES\n+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL\n+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA\n+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\n+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\n+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP\n+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES\n+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI\n+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA\n+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL\n+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG\n+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP\n+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES\n+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL\n+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA\n+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV\n+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG\n+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP\n+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS\n+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL\n+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA\n+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI\n+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG\n+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP\n+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS\n+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL\n+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA\n+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-\n+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI\n+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL\n+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS\n+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA\n+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK\n+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK\n+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]\n+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL\n+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV\n+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL\n+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT\n+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP\n+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN\n+> 8=opsin, greensensitive human (fragment) S07060\n+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP\n+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS\n+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC\n+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]\n+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM\n+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV\n+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA\n+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL\n+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH\n+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS\n+VSPA\n+> 10== Z68193 1 human Red Opsin <>[]\n+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM\n+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV\n+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS\n+AVWTAPPIFGWSRYWPH"..b"ISIDR\n+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT\n+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE\n+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC\n+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK\n+LAERPERPEFVLQNADYCRKKGHDS\n+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]\n+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL\n+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM\n+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW\n+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV\n+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL\n+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC\n+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT\n+> 31=p A47425 serotonin receptor 5HT-7 - rat\n+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL\n+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM\n+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW\n+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV\n+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL\n+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC\n+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT\n+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]\n+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA\n+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC\n+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED\n+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT\n+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN\n+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP\n+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC\n+RQ\n+> 33=p A35181 serotonin receptor class 1A - rat\n+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA\n+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC\n+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED\n+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT\n+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN\n+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP\n+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC\n+RR\n+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\n+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS\n+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV\n+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT\n+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP\n+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE\n+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA\n+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK\n+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL\n+NPIIYTIFSPEFRSAFQKILFGKYRRGHR\n+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS\n+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV\n+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT\n+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP\n+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE\n+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA\n+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK\n+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL\n+NPIIYTIFSPEFRSAFQKILFGKYRRGHR\n+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR\n+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV\n+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM\n+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI\n+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI\n+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR\n+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT\n+VFSPEFRHAFQRLLCGRRVRRRRAPQ\n" |
| b |
| diff -r 6f28e90db932 -r bf28a8cff401 test-data/sample_nuc.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_nuc.fa Wed Mar 20 07:34:52 2024 +0000 |
| b |
| @@ -0,0 +1,41 @@ +>MZ681498.1 Rotylenchus bunae isolate GE29E-RO6 small subunit ribosomal RNA gene, partial sequence +ATGCATGTATAAGTATAACCTGCCAGACAGGGAAACTGCGGACGGCTCATTACAACAGCCTTAATTTACT +TGACCTTGACAACCTACTTGGATAACTGCGGTAATTCTGGAGCTAATACATGCACCAAAGCTCCGATCCC +TCGTGGAGAGGAGCGCATTTGTTCGCCACAAAACCAAACGCCCCACAAGGGCGTTCAGTGTTGACTCAGA +ATAACTAAGCTGATCGCACGGTCTTGCACCGGCGACGTGTCTTTCAAGTGTCTGCCTTATCAACTTTCGA +TGGTAGTGTATCTGCCTACCATGGTTGTGACGGGTAACGGAGGATAAGGGTTCGACTCCGGAGAAGGGGC +CTGAGAAATGGCCACTACGTCTAAGGATGGCAGCAGGCGCGCAAATTACCCACTCTCAACACGCTGAGGA +GGTAGTGAAGAGAAATAACGAGACCGTTCTCACATGAGGCCGGTCATCGGAATGGGTACAACTTAAACCC +TTTAACGAGTATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCAAAATGCAT +AGAATTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTGTGCTGGCCGCCCGGTCTGCTCGCTGAGCAC +GCACTGGTGCGGTCGGCTTTCCTGCCCGGTACCTCCCCGGCGTTGGCCTTCACCGGTCGGCGTCGGTGGC +CGGGCGAGTTTACTTTGAACAAATCAGAGTGCTTCAAACAGGCGTTTCGCTTGAATGTTCGTGCATGGAA +TAATAGAAGAGGATTTCGGTCCGATTTTGTTGGTTTTGCTGACCGAGATAATGGTTAACAGAGACAAACG +GGGCCATTCGTATTGCTACGTGAGAGGTG + +>MZ681497.1 Rotylenchus bunae isolate GE29A-R1 small subunit ribosomal RNA gene, partial sequence +CTGCGGACGGCTCATTACAACAGCCTTAATTTACTTGACCTTGACAACCTACTTGGATAACTGCGGTAAT +TCTGGAGCTAATACATGCACCAAAGCTCCGATCCCTCGTGGAGAGGAGCGCATTTGTTCGCCACAAAACC +AAACGCCCCACAAGGGCGTTCAGTGTTGACTCAGAATAACTAAGCTGATCGCACGGTCTTGCACCGGCGA +CGTGTCTTTCAAGTGTCTGCCTTATCAACTTTCGATGGTAGTGTATCTGCCTACCATGGTTGTGACGGGT +AACGGAGGATAAGGGTTCGACTCCGGAGAAGGGGCCTGAGAAATGGCCACTACGTCTAAGGATGGCAGCA +GGCGCGCAAATTACCCACTCTCAACACGCTGAGGAGGTAGTGAAGAGAAATAACGAGACCGTTCTCACAT +GAGGCCGGTCATCGGAATGGGTACAACTTAAACCCTTTAACGAGTATCTATGAGAGGGCAAGTCTGGTGC +CAGCAGCCGCGGTAATTCCAGCTCTCAAAATGCATAGAATTATTGCTGCGGTTAAAAAGCTCGTAGTTGG +ATCTGTGCTGGCCGCCCGGTCTGCTCGCTGAGCACGCACTGGTGCGGTCGGCTTTCCTGCCCGGTACCTC +CCCGGCGTTGGCCTTCACCGGTCGGCGTCGGTGGCCGGGCGAGTTTACTTTGAACAAATCAGAGTGCTTC +AAACAGGCGTTTCGCTTGAATGTTCGTGCATGGAATAATAGAAGAGGATTTCGGTCCGATTTTGTTGGTT +TTGCTGACCGAGATAATGGTTAACAGAGACAAACGGGGCCATTCGTATTGCTACGTGAGAGGTGAAATTC +TTGGACCGTAGCAAGACGGACTACAGC + +>ON855043.1 Rotylenchus sp. JQ-2022 internal transcribed spacer 1 and 5.8S ribosomal RNA gene, partial sequence +GGCCGTCACTCCGGGGGGACAACACAAACGCCCTGAGGGCTTTACTCGTTGGGGTGCAAACTGGATCGAG +TGGCGCACACATCCCTTCCACGCAAAGACCTGCTGAAGAGGTCGGAGGCGATGAGTCCGAGCAACCCCAC +AAGCAACCAGGTTGGGGAAGCTGCACACGATACTGGGATGCACGCCCCCAGGGCACCTAACGGCTGCCGC +TGGCGTCTGTGCGTCGTTGAGCAGTTGTTGCGCACTTGCTTTTGTCGGAGCTGTACTCGGAGCATGCTGG +CATGGACCCACACAAAAGTGTGTGGCAGCGGCCACACACCCCTGTCCATGTCCTACGGACCGTAGCTAGG +GCGTGCTCTGGGTTTCTTCGGCTGGCAGTGTTGCTACGTCCGTGGCTGTGATGAGACGACGCGGTAGGGC +CTTGTGCGATGCGCCTGCACTTGGCTTAAGACTTGATGAGCTCACTGCGAAGAGCCGCCAGCAACCTTTT +TTTCATATACATTTTTTACAGGCACACTTGTGTGCTGATGAACAAAAATTCTAGCCTTATCGGTGGATCA +CTCGGCTCGTAGGTCGATG + |