| Next changeset 1:1ac6ee298657 (2022-03-28) |
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Commit message:
"planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" |
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README.rst phykit_alignment_based.xml phykit_alignment_tree_based.xml phykit_tree_based.xml test-data/12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit test-data/12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit test-data/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit test-data/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile test-data/Steenwyk_etal_mBio_2019_EOG091N44MS.aln.fa test-data/alignment_list_for_create_concat_matrix.txt test-data/out.fa test-data/out.occupancy test-data/out.partition test-data/output test-data/simple.fa test-data/test_alignment_0.fa test-data/test_aln_pk_pi.txt test-data/test_aln_pk_pi_verbose.txt test-data/test_aln_pk_pis.txt test-data/test_evo_rate.txt test-data/test_tree_simple_pd.txt test-data/test_tree_simple_pd_verbose.txt test-data/test_tree_simple_rfd.txt test-data/test_treeness_over_rcv.txt test-data/tree_simple.outgroup.txt test-data/tree_simple.pruned test-data/tree_simple.tre test-data/tree_simple.tre.pruned test-data/tree_simple.tre.rooted test-data/tree_simple_keep.pruned test-data/tree_simple_other_topology.tre test-data/tree_simple_prune.txt test-data/tree_simple_prune_keep.txt |
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| diff -r 000000000000 -r 37b049bf729a README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Mar 28 16:23:18 2022 +0000 |
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| @@ -0,0 +1,5 @@ +PhyKIT +======= +PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data. +PhyKIT helps process and analyze multiple sequence alignments and phylogenies. +Generally, all functions are designed to help understand the contents of alignments (e.g., gc content or the number of parsimony informative sites) and the shape of trees (e.g., treeness, degree of violation of a molecular clock). \ No newline at end of file |
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| diff -r 000000000000 -r 37b049bf729a phykit_alignment_based.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phykit_alignment_based.xml Mon Mar 28 16:23:18 2022 +0000 |
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| @@ -0,0 +1,126 @@ +<tool id="phykit_alignment_based" name="PhyKit - Alignment-based functions" version="0.1.0" python_template_version="3.5"> + <requirements> + <requirement type="package" version="1.11.7">phykit</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + #if $tools.tool_selector == "create_concat" + #import re + touch 'aln_list.txt'; + #for $input in $tools.input1 + #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier) + ln -s '$input' $safename && + echo '$safename' >> 'aln_list.txt'; + #end for + phykit create_concat -a 'aln_list.txt' -p 'out'; + cp out.fa ${fasta} ; + cp out.partition ${partition} ; + cp out.occupancy ${occupancy} ; + #elif $tools.tool_selector == "pairwise_identity" + phykit pairwise_identity $tools.input1 $tools.verbose > $pairwise_id; + #elif $tools.tool_selector == "parsimony_informative_sites" + phykit parsimony_informative_sites $tools.input1 > $parsimony_informative_sites; + #end if + + ]]></command> + <inputs> + <conditional name="tools"> + <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)"> + <option value="create_concat">Concatenate alignments.</option> + <option value="pairwise_identity">Calculate the average pairwise identity among sequences</option> + <option value="parsimony_informative_sites">Calculate the number and percentage of parismony informative sites</option> + </param> + <when value="create_concat"> + <param name="input1" type="data" format="fasta" multiple="true" label="alignment list file. File should contain a single column list of alignment sequence files to concatenate into a single matrix." optional="false" /> + </when> + <when value="pairwise_identity"> + <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" /> + <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False" label="optional argument to print all pairwise identities" /> + </when> + <when value="parsimony_informative_sites"> + <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="fasta" format="fasta" label="Concatenated fasta alignment file"> + <filter>tools['tool_selector']=='create_concat'</filter> + </data> + <data name="partition" format="iqtree" label="A partition file ready for input into RAxML or IQ-tree"> + <filter>tools['tool_selector']=='create_concat'</filter> + </data> + <data name="occupancy" format="txt" label="An occupancy file that summarizes the taxon occupancy per sequence"> + <filter>tools['tool_selector']=='create_concat'</filter> + </data> + <data name="pairwise_id" format="txt" label="Summary statistics unless used with the verbose option in which all pairwise identities will be reported."> + <filter>tools['tool_selector']=='pairwise_identity'</filter> + </data> + <data name="parsimony_informative_sites" format="tabular" label="three tab delimited values: col1: number of parsimony informative sites col2: total number of sites col3: percentage of parsimony informative sites"> + <filter>tools['tool_selector']=='parsimony_informative_sites'</filter> + </data> + </outputs> + <tests> + <test> + <param name="tool_selector" value="create_concat" /> + <param name="input1" value="12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit,12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit,12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit"/> + <output name="fasta" file="out.fa"/> + <output name="partition" file="out.partition"/> + <output name="occupancy" file="out.occupancy"/> + </test> + <test> + <param name="tool_selector" value="pairwise_identity" /> + <param name="input1" value="test_alignment_0.fa"/> + <param name="verbose" value="false" /> + <output name="pairwise_id" file="test_aln_pk_pi.txt"/> + </test> + <test> + <param name="tool_selector" value="pairwise_identity" /> + <param name="input1" value="test_alignment_0.fa"/> + <param name="verbose" value="true" /> + <output name="pairwise_id" file="test_aln_pk_pi_verbose.txt"/> + </test> + <test> + <param name="tool_selector" value="parsimony_informative_sites" /> + <param name="input1" value="test_alignment_0.fa"/> + <output name="parsimony_informative_sites" file="test_aln_pk_pis.txt"/> + </test> + </tests> + <help><![CDATA[ + +Version: 1.11.3 +Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096 +Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-based-functions +Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675 + +PhyKIT helps process and analyze multiple sequence alignments and phylogenies. + +Generally, all functions are designed to help understand the contents of alignments +(e.g., gc content or the number of parsimony informative sites) and the shape +of trees (e.g., treeness, degree of violation of a molecular clock). + + +Alignment-based commands +======================== +create_concatenation_matrix (alias: create_concat; cc) + - create concatenation matrix from a set of alignments +pairwise_identity (alias: pairwise_id, pi) + - calculates average pairwise identify among sequences in + an alignment file. This is a proxy for evolutionary rate +parsimony_informative_sites (alias: pis) + - calculates the number and percentage of parsimony + informative sites in an alignment + + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubPhyKIT, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {PhyKIT}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/JLSteenwyk/PhyKIT}, +}</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 37b049bf729a phykit_alignment_tree_based.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phykit_alignment_tree_based.xml Mon Mar 28 16:23:18 2022 +0000 |
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| @@ -0,0 +1,67 @@ +<tool id="phykit_alignment_tree_based" name="PhyKit - Alignment- and tree-based functions" version="0.1.0" python_template_version="3.5"> + <requirements> + <requirement type="package" version="1.11.7">phykit</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $tools.tool_selector == "treeness_over_rcv" + phykit treeness_over_rcv -a $tools.input1 -t $tools.input2 > $treeness_rcv; + #end if + + + ]]></command> + <inputs> + <conditional name="tools"> + <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)"> + <option value="treeness_over_rcv">Calculate treeness/RCV for a given alignment and tree.</option> + </param> + <when value="treeness_over_rcv"> + <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" /> + <param name="input2" type="data" format="newick" multiple="false" label="Tree file" optional="false" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="treeness_rcv" format="tabular" label="Three tab delimited values: col1: treeness/RCV col2: treeness col3: RCV" > + <filter>tools['tool_selector']=='treeness_over_rcv'</filter> + </data> + </outputs> + <tests> + <test> + <param name="tool_selector" value="treeness_over_rcv" /> + <param name="input1" value="simple.fa"/> + <param name="input2" value="tree_simple.tre"/> + <output name="treeness_rcv" file="test_treeness_over_rcv.txt"/> + </test> + </tests> + <help><![CDATA[ + +Version: 1.11.3 +Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096 +Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-and-tree-based-functions +Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675 + +PhyKIT helps process and analyze multiple sequence alignments and phylogenies. + +Generally, all functions are designed to help understand the contents of alignments +(e.g., gc content or the number of parsimony informative sites) and the shape +of trees (e.g., treeness, degree of violation of a molecular clock). + + +Alignment- and tree-based commands +================================== +treeness_over_rcv (alias: toverr) + - calculates treeness/rcv, treeness, and rcv + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubPhyKIT, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {PhyKIT}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/JLSteenwyk/PhyKIT}, +}</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 37b049bf729a phykit_tree_based.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phykit_tree_based.xml Mon Mar 28 16:23:18 2022 +0000 |
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| b'@@ -0,0 +1,157 @@\n+<tool id="phykit_tree_based" name="PhyKit - Tree-based functions" version="0.1.0" python_template_version="3.5">\n+ <requirements>\n+ <requirement type="package" version="1.11.7">phykit</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ #if $tools.tool_selector == "evolutionary_rate" \n+ phykit evolutionary_rate $tools.input1 > $evo_rate;\n+ #elif $tools.tool_selector == "patristic_distances"\n+ phykit patristic_distances $tools.verbose $tools.input1 > $patristic_distances;\n+ #elif $tools.tool_selector == "prune_tree"\n+ phykit prune_tree $tools.input1 $tools.input2\n+ -o \'out.pruned\'\n+ $tools.keep;\n+ cp out.pruned ${pruned_tree_out};\n+ #elif $tools.tool_selector == "robinson_foulds_distance"\n+ phykit robinson_foulds_distance $tools.input1 $tools.input2 > $rf_distance;\n+ #elif $tools.tool_selector == "root_tree"\n+ phykit root_tree $tools.input1 \n+ -r $tools.input2\n+ -o \'out.rooted\';\n+ cp out.rooted ${rooted_tree};\n+ #end if\n+\n+ ]]></command>\n+ <inputs>\n+ <conditional name="tools">\n+ <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">\n+ <option value="evolutionary_rate">Calculate a tree-based estimation of the evolutionary rate of a gene.</option>\n+ <option value="patristic_distances">Calculate summary statistics among patristic distances in a phylogeny</option>\n+ <option value="prune_tree">Prune tips from a phylogeny</option>\n+ <option value="robinson_foulds_distance">Calculate Robinson-Foulds (RF) distance between two trees</option>\n+ <option value="root_tree">Root phylogeny using user-specified taxa</option>\n+ </param>\n+ <when value="evolutionary_rate">\n+ <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />\n+ </when>\n+ <when value="patristic_distances">\n+ <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />\n+ <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False" label="optional argument to get all distances" />\n+ </when>\n+ <when value="prune_tree">\n+ <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />\n+ <param name="input2" type="data" format="text" multiple="false" label="Single column file with the names of the tips to remove from the phylogeny" optional="false" />\n+ <param name="keep" type="boolean" truevalue="--keep" falsevalue="" checked="False" label="Instead of pruning tips in list of taxa, keep them" />\n+ </when>\n+ <when value="robinson_foulds_distance">\n+ <param name="input1" type="data" format="newick" multiple="false" label="Tree 1" optional="false" />\n+ <param name="input2" type="data" format="newick" multiple="false" label="Tree 2" optional="false" />\n+ </when>\n+ <when value="root_tree">\n+ <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />\n+ <param name="input2" type="data" format="text" multiple="false" label="Single column file with taxa names to root the phylogeny on" optional="false" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="evo_rate" format="txt" label="total tree length divided by the number of terminals.">\n+ <filter>tools[\'tool_selector\']==\'evolutionary_rate\'</filter>\n+ </data>\n+ <data name="patristic_distances" format="txt" label="summary statistics of all tip-to-tip di'..b'ce and col 2: the normalized RF distance" >\n+ <filter>tools[\'tool_selector\']==\'robinson_foulds_distance\'</filter>\n+ </data>\n+ <data name="rooted_tree" format="newick" label="Rooted tree">\n+ <filter>tools[\'tool_selector\']==\'root_tree\'</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="tool_selector" value="evolutionary_rate" />\n+ <param name="input1" value="12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile"/>\n+ <output name="evolutionary_rate" file="test_evo_rate.txt"/>\n+ </test>\n+ <test>\n+ <param name="tool_selector" value="patristic_distances" />\n+ <param name="input1" value="tree_simple.tre"/>\n+ <param name="verbose" value="false" />\n+ <output name="patristic_distances" file="test_tree_simple_pd.txt"/>\n+ </test>\n+ <test>\n+ <param name="tool_selector" value="patristic_distances" />\n+ <param name="input1" value="tree_simple.tre"/>\n+ <param name="verbose" value="true" />\n+ <output name="patristic_distances" file="test_tree_simple_pd_verbose.txt"/>\n+ </test>\n+ <test>\n+ <param name="tool_selector" value="prune_tree" />\n+ <param name="input1" value="tree_simple.tre"/>\n+ <param name="input2" value="tree_simple_prune.txt"/>\n+ <param name="keep" value="false" />\n+ <output name="pruned_tree_out" file="tree_simple.pruned"/>\n+ </test>\n+ <test>\n+ <param name="tool_selector" value="prune_tree" />\n+ <param name="input1" value="tree_simple.tre"/>\n+ <param name="input2" value="tree_simple_prune.txt"/>\n+ <param name="keep" value="true" />\n+ <output name="pruned_tree_out" file="tree_simple_keep.pruned"/>\n+ </test>\n+ <test>\n+ <param name="tool_selector" value="robinson_foulds_distance" />\n+ <param name="input1" value="tree_simple.tre"/>\n+ <param name="input2" value="tree_simple_other_topology.tre"/>\n+ <output name="rf_distance" file="test_tree_simple_rfd.txt"/>\n+ </test>\n+ <test>\n+ <param name="tool_selector" value="root_tree" />\n+ <param name="input1" value="tree_simple.tre"/>\n+ <param name="input2" value="tree_simple.outgroup.txt"/>\n+ <output name="rooted_tree" file="tree_simple.tre.rooted"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+Version: 1.11.3\n+Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096\n+Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#tree-based-functions\n+Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675\n+\n+PhyKIT helps process and analyze multiple sequence alignments and phylogenies.\n+\n+Generally, all functions are designed to help understand the contents of alignments\n+(e.g., gc content or the number of parsimony informative sites) and the shape\n+of trees (e.g., treeness, degree of violation of a molecular clock).\n+\n+Tree-based commands\n+===================\n+evolutionary_rate (alias: evo_rate)\n+ - reports a tree-based estimation of evolutionary rate for a gene\n+patristic_distances (alias: pd)\n+ - calculate all pairwise distances between tips in a tree\n+prune_tree (alias: prune)\n+ - prune taxa from a phylogeny\n+robinson_foulds_distance (alias: rf_distance; rf_dist; rf)\n+ - calculates Robinson-Foulds distance between two trees\n+root_tree (alias: root; rt)\n+ - roots tree on user-specified taxa or taxon\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+@misc{githubPhyKIT,\n+ author = {LastTODO, FirstTODO},\n+ year = {TODO},\n+ title = {PhyKIT},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/JLSteenwyk/PhyKIT},\n+}</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 37b049bf729a test-data/12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit Mon Mar 28 16:23:18 2022 +0000 |
| b |
| b'@@ -0,0 +1,744 @@\n+>Kpol\n+ATGTAATGTTAGATCTTTTAAAGGAGGCTAAAAATGGCTTGTAGAGGAATTTGAAGAAGC\n+TAAGAATATTAAGGGGTTGAAAGGAAGAAAATAATATTTTGCTTGTGTTTATGGGTAAAG\n+TACCCTGC---------ATAGCTAATTGCGAAGAGGCTTTGAATAGTATATAAGGGCTCT\n+GAATTGGTAGTCAAATGTTTGGTTGGAAAGGTCTATTTTATGTAAACTCAAACAT-GTTT\n+ACCAACTATCCACTTTTAATACTTCGATTTATGTGGTGTTATTCCAATGTGTTATATACG\n+GGCTGCCATTGGTCATTTGTTCATGAAATGAGAACAATTAGGAAATATCCTTGTGAAGAA\n+TATTCCTAAGACATATGTGCTGGTTGCAAGGCGACTATCTAAATTTATCCTCCACAGATG\n+TCTCTCAAATTGTAAGATAATTAATTCTAAAGAGAAAGAACAAGTTTCAAAATTCAAGAG\n+AAAGATTGAACTAAGTGCTATGATCCATTATCCACAAAATTAATTCATGGCTTGGGAGGT\n+TTATCAATTCAGTGCGAGATCTATCCCAATTGATTAATTTTCTGATATGATGAGAGAGTC\n+GAAATTTGAAGAAGAGTTAATCATAGTCTTTTTGAGTCAATGCCAATTCTAAGGGATCAT\n+ACTCCAGAGTAAATCGATTGGAGTGGTCTATTGTACTAGTCGAAAAGGTGGAACTTTATT\n+TGAATGGCAAGATGTACTGACTGAATTCTTTGGATGGACAAAAGTAAGAATATTTTATGT\n+TCCCAAAGGAACCATTGCAGTTTACTATAGATGGGATGTTCAAATATTCTTCTTACACAT\n+AAAACAATTAACACAACAGGTAAGGATGAACCTCAAGCCATTAAA---------------\n+-----TGAACCA-----------------GATATGACAGAATTGACGTCTACTGTAGAAT\n+GACAAAATGAATA-------ATACCAGCATTATTGGAACTGTATTTTAGAAACCCTTTGG\n+AAATATATCAAGCAAAACTGTATCATTCTTAAGAATAATTCCATATCTTATTGTCTCGGA\n+ATATGTGTGCACATTTTAAATCTGGTAATCATTAAAGCATTCGATTGATTAGGTGCACAT\n+TTAATTAATTAAAATTGCATTACTTTAGATCTTGCTCCGCATACACTTATTCGATGTAAA\n+CTACAAAAGCGTTAAGTTTATTCGATAGGTCCTATCCAAGATGATTTAATGCTAGAGTAA\n+ACTAGGTAAGCTGATTTCATGGAAAAGAAACTGGAAGAGCTAAAACGTTCTTATCTGATT\n+GCTGAAATTTCAGCTAGATATTTAACGTAGGTTGGAGTGAGCAACCTCGAATCATGATAA\n+GTCTTGAAATTTTCAATAATGTTCTAATAGTTAGAGGTTTGAATAGACATGTATAAGGGC\n+CAATTATTGGGACAAGCCAAACATTTTACTATCAAGAAGAG-TTAAAGATAACTGATAGT\n+GACATGAATACGTAAATTAGCTTATATGCTAATCCTTCATTAAAGGACA---GATCTTTC\n+AAAATCTTATTTACTTTGGGTGATTTTATGCAAATTTTACGTGATACAAAAGGGCATCGG\n+CTGTACATGCATTTGAATTAGATTCAGATATCGTTCACAAAATATGGTCGAGCATATTTA\n+ACAGTGGAAATTGGTCGTGCAGAATCAATCTCAAAACTTAGTTAAACCGATGGTAAAGAA\n+ATATTTAAGGTATACATGTTGGCCATTTGATTATAGGTTTGTATTAAGGACAACAAGGAG\n+CTCATTAATGGTTCCAATGCTTTCGTATTGAACGATAGTCGAATCGTGGGTTGATTAGGT\n+CAGTCTTATTTGAGTTGCGGCAGAATAGAAGCCTCTTAAGTATTGAAAGCAAGATTAGAT\n+CCGATCACCTGTTGCAAAATTTAGACAATCCCTTCAGAGATGGTATATGTTAGTATTTCT\n+AATTTGGAATAATAATGGAAACCCAAAGGAAATCATTCCAAGTTCAACTCAGAAACTTTG\n+ATGAATGCCCAGATTATTTAATCAGGATTTTTAACAAAGTCTGATAATGCTTTGAGGCAA\n+TTTCTGTTTGAGTTATATTGCGACAGATGAATCTTTCCCACAATCATGGCATCTTTTTCT\n+CTGCATTGAAATATTTATTCTAGTCGATCAAAGGATAAGTTACCAATAGAAACGTATTTC\n+GATTTTTGAAAATTGTAAAATAAAAGACGTATCAAATCAGATTCGATGGTGTACCACTAC\n+ATTGCTAACT---ACCGCTGATTATGTGGATAACAGCCATTCTGATTTTAGTGCTAAATG\n+TGCAATTTAACTGGTAATATTGATCAAGCTAAGATTTAAAGTATCACTGTGGCATAATTT\n+AGGATGGCCGAGCTCATTTCTTATTAACATAATAATAAGAAAGAACGATCTTCTGCTTTA\n+AGAAGTATTAATATCAACAAATAGTTTTATCCTGGGTAGTTTAGGATTGCACTATGGATG\n+CAATTGGAAAGTCTCTCAGCATTGTTTATAAACGATTGTTAGCACCAAGAAGCTCTTTGT\n+TTCTGGCTGTTCTTCATTGAACAGACGAATTGAATTTCACGTCAAGTCAATCAAGGTTAC\n+AGATATAGCCCCACAGTCCTACAGGCTTGGTATGGATTAGTA------------------\n+------------------------------------------------------------\n+---------------------NNNNNNNAGTAAGTGAAAGATATAGTACATCAGACAGTT\n+GACCTCCGTTGCATATGGTCTAGAACAGTATTCAAAAAGAGTCGGTGTGATTGCCTTACA\n+ATTCTATTAACATTGGAAAGATTACATTTGTTTTCTAACCAAATGGTGGTGTAGACTATC\n+TACATTTGGAAAAGATTGAAAGAAAGAGAGATCGAGTTATTTGCATATAAATCTCAGTTC\n+AAGAATTCAATTAGCTGGAAATTATAGAATTCATGAATCTGAACTATCTGTGATTATCTC\n+GGTACAACAACGAACAATCACTTCAAGCCCAAACTCGAATATTCGCCTAGGTCTAAGTAA\n+TCTCCAGATAATGATGGCATTGAACTATTTCCAACTTTGTACAAATAAAATAAGCATTTA\n+ATTTACTGATTTCAACATATTATCGATATTGGTTTAGAAGAAACTAAAAATCGCCTTGGA\n+TGAATTGATGAATACATTCAACCATTAACGAATTTTTGGGTCTGGTTATAGAATGTCGTA\n+TTAGACACATCAAGTTATTACCAAAATTATTGAATGTTAGAGGTACCACATTTCTAGATT\n+AAAGAAAAACAGATATACTTATTTGTATTGAATCAACAAAAGATTAGAAAAGAAAAATTG\n+TCTCCGAATTATCTATTTGGAAGACCTTACTTTCCAAACGTGCAATTCTTGGAAGCCTGT\n+AAATAGAAGATAGTCTCAGAGTATCCACAGAAGCTAGTTCACCATTTAGCAAGACCTGCG\n+AAATGAAGTTATACATTCAAGGTTTTCCTATCACCTTGGTACAAAATTGTTCTCGCATTA\n+AATAGTGTTTT--\n+>Kpha\n+ATGGTATCTGGCAGCTTTTGAAAGAGGCAAAATCAGGGTAGTAGAGGTATTCGAGGAGGC\n+TATGATTCTTAACAATTTGATTGGATAAGCACAATACTTTGCCTGTATTCTTAGGGAAGT\n+AATCTTGTTT--CGTGAATTTCTAAGCAAGAAAATGCAATTTCTGCTATAGGGAAGCTTT\n+GATTCTATTTTCAAATTACTAGATGGAAAGGGTTATTCAGCTTTG'..b'AAGACAGACGCGCATATTTGTAGAGAGTTACAAAAAGGCTTCATTTTAATGAT--\n+--ACCGGTAAACAAGTATGGAAGAGTCACTTTCCCAAATATCTGAGGTTTGGGAGATGCT\n+AAATAGACTATCAACGTAGAATAGCATCTGTGTCCAGTGCGAAGTATGGATATTGCTGTG\n+AAACTAAATTAAGCGTTCAGGATGTTTCTATGCCCTTGATGCATCTGAGTGCAAGCTTTA\n+AGGAATGTTTC--\n+>Scer\n+ATGTGGTATTACAGCTATTGAAGGAAGCCAAACAAGATTGAAAATCGTACTTGAAGAGAC\n+CACGAATATGGAAGGTCTTACTAGATCCCGATAATATTTCGCACATTTTTCTAGGGAAAG\n+ATTCGAGTCTGTTTCAGTCAAATCGGCCGGAGAGAGCTACTAATCATACGTGTCCGCTCC\n+AAATTAGTTTGATAACCTTTAGGTGGAAAGGACTTTTTCCTATTAGAACCACTAG-GTGT\n+CCCAGACTACTTCGTATGATATTTTGACCTGTGTGGCCATATGCAGACGCACTTTAAGCG\n+GACAGTCTCAAGTAAACTATAAATGACATAAAATTACTAAAGACGCATCCATGTCAAAAA\n+GCTTTTATCAGCATTTGAACTGGGTGCTAGGGGACTATTTCTACTATCTCACCCCGGCGC\n+TTTATTAATCTTTAAGATACTGTCTAATATTGAAACAACGGAAATAGGTAGACCTACAGA\n+ACAGGTTAAACTAAAAGCTGTGATCCTGATTTCATTAACTAAATTCATCTCCTGGGAAAT\n+AATTAAATTCAGAATGACAGTTATCCCAGTTGGTAAATTTCTCGCTACGATCAAAGAGAG\n+TGAAATTGAGAACCAGTTAAATATAGTCATGCTAAATCAATGCCGCTGGAAAAAAAGATT\n+TTTCACGAGTTAGGAAATTCGAGTGGTCTTTGATCATCATCTGCTTGATGGCAAAGTATT\n+CGAATGGACAGATACGAAGACTGGACAACATGGATGCCCCATGATAAAAGTACTTTAGAT\n+TTCCTAAAGATCCATTGCCATGTCCTCTATCTGGCTTCCTCAAACTATCGAAATATATAT\n+TAAAAGTTTGGATCGGCTAATAAACCACCTGAAGGCCATAAAAAGACGGAAACAGATAGG\n+ATGTATGAGACAAATGAGATGATAAAGATGTTGAAGATGAGTTAAGTGATAGATGGGGGC\n+AAAGAGATGAAGAGACCTATGAAATTGGTTTATTAGAGAAGGGTTGTCACTGTATTGCGG\n+AGATATCGTAATGTAAAATATATCTTACGCACGCATTCTTGTATATCCTACTGACCAGGA\n+GTATGGGAGCTTAACTCAAAAATGGTATTCTTTAATGCCATATATAAGCTGGGGGTACAT\n+TTGCCATTAAAAAAAGGAATTTCTCTGGATTTGGCTCCGTTTATACATAGTCGATGCAAG\n+GCACATGTGCATTAAAGTTATATGATACATTTTATCCGTGATTTAGTAATATACAAGAAA\n+AATGGGCAAGATAATTTTATTGAAAGAAAATTGGAGGTGCTATGACATTACTAACACGTG\n+CATGACACGCCTATCGGAAGTTTATGACGTCATGGAGTAAGCCCTATGGTTTATGGACGG\n+GATTAGCTGGCTTAGATACTGTCATCAGGGTTCAAGGTTGGATACTTCGATATTCGGATT\n+AAACTTATGGGGCAAGCCAAGTTTCATTATG------GCAT-GCTTCCATTAACGATGCT\n+AAACAGGAAACGTCAGTGCGCATTCATACTCATTCGAGTATTAAAAATG---GACTTTGC\n+TCCCGGATTTTGACACTGGGCGATTTTATTGCCACTTTATAAGACCATTTGGGGCCTCAA\n+ATGTATTCACTTTCGATCTGGATGGGGATTACACACACGAAGTATTACCGAACTTATGAA\n+GCAAGCCCAATTGGCAATGCTTCTTCCATCGCTTCAATTAATTAAGGTGAAAAAAAAGGC\n+AGAACTGCGCTCAAATAACTGGCCCTTTGGTCGTAGGGTTGTCTTGAAAGCAAGAAGAAG\n+TTCTTTAGTGGTTTCAATGCTTTCGTGTTGATCAATAGTAGAGTCATGGGTGGCCTGGGA\n+CAAGCATACCACGCGTGTGGTCGTATAGAAGCATCTCAAGTTTTGACAGCATCATTAAGG\n+CCTCTCATACTTTGCCCAACTTAGTATTTCTCATGTGACGTAGTATATCTTGATTTAGAC\n+ATCTGGAGGTATGTCAAGAAGCCGTACAGAAGTCATTCCAAATGGTTAGTGGAAGTGCTT\n+ATGAATTCCTTGATTATATTCGCAGGGTTCTTGCTCAAATCAGTTAATGCAAGGACACTA\n+TTGAACGGTCAAGATAATTATCAGTGAAAAAATTGAGAACACAGGTTGGACTACTTTCAC\n+AAGTACTGAGATATTTATTTGGATAGGTCAAGGTATACTTTACCTGTTGAATACTATATC\n+AATTTTTGAAAATTCTCAATTTTCTGGTAGTGAAAATTATCTTCGACAATACAAAACGTC\n+TTTACTCGATAGCACTACTGATTATGGTCATTGCGGCAGTTTTGATCTTAGTTCAAAATA\n+TAGTGTTTGGATCAAAAATTTACAGATATAGAGAGGTCAGGGCTCATACTGGTATAATAT\n+AGGATCTCAGAGCTTACTGCTTTCAAACATGAACCGCAGAAGAATCTATTTTTGCTTTTA\n+AGAATCATTCATTACAGCTAATACAAGTAACTTGGATTGTCTAGGATAGCACTATGGACA\n+CAACTTTCGTGTCTCTCAACATTGCTTATTAACAACTGTTGGAACCGAAGCGCAATCAGT\n+TCCTGGCTATGCTAGTTTAAGAAAAGGAACTGAATTTCTCAACAGGTTCGAATAAATTAC\n+AAACCTTGCCCCACAGTCGTACTGGCTAGGTATGGCTTGATTCTTGAGGAACAAGCATTA\n+TCAAGTTCTAACTTTTGACACTCCTTCAATTTCTAAGGAGGTCAGGCTCGCAATTATGTT\n+GCTAAAATGTCCTTGAGTCACAAATAATGGTGCGTGAAAGATATTGGACAGTGGAAAACT\n+AACCACTGCTTCAATAGCTTTAGAGCAGTTTTCAAAAAAAGTCTGTATCATTGCTCTTCA\n+ATTCTTCTAACTCTTGAAAGGTTACATCACTATGAAAATCAAACGACGGTATCGGTTGAT\n+AGGCTTTGGAAAAAGTTGAGAAAAAGAGAAAGAGAACTGTTTGCGAATTAAGGACAATCC\n+TCGTATTCACTTAGTTAGAAATTTCGACTCTTATGAACCTGATCTTTCTCAGATTATATC\n+TGACGAGCGACGAAAAATCAATGAAAACCAAAAATCCAATCCTTGCTTAGGATTAAGTTA\n+TCTCTAAACGACGATCGCTTTGAACCAATTCCAGAACTGCAAGCATAAGATTAGCACCTA\n+GTTGTTTAATTGGAAGGTGCTTTTGATGTAGGTGAATCTGACACAAAGGAATGCTTTACA\n+GGAACTAAAGAATATAAGCCACAACCGCAGACTTGTTAGAACTAGATTCAGTATGTCATT\n+CTAGACGTAGCGTAGATTTAAGCATTATTTTAGAAATTGAAGCTTGCCATACAAACAATA\n+ATAGAAAGACAGACGCACATATCTGTAGAGAATTACTAAGAGACTTTATCGTAACGAT--\n+--ACCGGTAAACAAGTATGGAAGGGTCACTTTCCCTAATACCTCAGGTTTGGGAGAGATT\n+AGATAGAATATCAACGAAGAATAGCTTCTATGACTAGTTCGAGGGATGGAAACTATTGTG\n+AGAGTAAGTTGAGCATACAAGATGTTTTTGTGCCCTTGACGTTACTGAGTGAAGGCGCTA\n+AACAATGTTTC--\n' |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit Mon Mar 28 16:23:18 2022 +0000 |
| b |
| b'@@ -0,0 +1,360 @@\n+>Kpol\n+ATGGCAGAGACA--------------------AGCACAAATGGGGTGCAGGATCT-----\n+----TCTCTACATT--------------ATTATCTAGCTTTTGATCATGGTGTTTCCTCT\n+TAGAGCAAAGAAATAAATCTGAACATTTTATATACTGAAATAGCCGTCAATTTAGGTAAG\n+AGCTGCAATTATTATAGGTGTATTGATGCAAAGGTAGATTAATAAAATAGTTGAATAATG\n+T-AGAGAAATGGATAGGAAAGTATTAAACTCATTATATTTAATTCAATTAAGATGTTAAA\n+TATTACACAGAACCACGTATTCTTAAAAGTTTAGATTACTTTCAACGAGATGGTAATTAT\n+TAGGTTGTATAGGAGATCTTAAGGAATTAATTCACGTTTC--------------------\n+-CATCTTCAATTGCAGTCAATCATTGAATATCTTATCTATTGGCTCGATTCCGTAATATA\n+TGTTTCAAACATCAAACAATGAAGAA-AGTGAGGATACTCAGCTTTCTTAATTGTGGAAA\n+TGTTATATAGCCATAAAGGATTCTCTTCCATTGTGACATTTGGATAATTATACCAAGGAA\n+TATTGCTTACCAGAACTAACTCTTCTGATTTGAGAAAGAACAGAAGCTAAAAATAAGCAA\n+AAGTGAATTTTTCACTATTTTACGAAGTCTGATGTTTCAAAGTATCTATTGATCATTGAC\n+TTCTTTGAGAATGTGGAAATATGGTCTTTGACTTCAATCTAAGGATTTTAAAATCAAGAA\n+GTAGCATTTGACTCAACCTAAAAGGGGGCTCTATTTCCTCACAAGTTTATAGTGCATTAC\n+AAGCAAGAACAACAAACCCGTAACCATATTATCAAAAACCGTTTACTTCAGGAATGAAGA\n+AATGGTATTGCCAAGATGATAATTACAGAAAAATGTAAATATTTTTCAATGCTTAGATAT\n+TGCAAGTCTTGCAGCTAGTCAGATCTTCGTGGATCTTGGCCTAAGAGTAAAA---TCCTC\n+AAAAAGACCCATGAATTCTACCCCAGAGGCTCCA----CCAAAGAAATTAAAAAAATGGT\n+TTCTTTCTCCACCTCCCCAAAAACATGCATAGAGGATCAGATGAGACATGATATGTACAT\n+GATAATAGAT----TATGGATTTTACTACGAGACACTATCCACATCTATTAGTTTGATCA\n+ATGTCTTTGAAATTATTAACATAAAAAAGTTCTAAGGGAATCAACCTGTATATTGTTCCA\n+TATTCAGTTATGCCTGCATACGCCAAGTATATATGATATTTATCTCTACCTTAGGCTCAG\n+CAGCGTGTTCGTGTTGTATTGTTAAAATAAGTTGTGCTGAAAAGGTTATTAATTCTACTG\n+CATGATGAGAAAAGATATTCGTCTCTATTCATCTTAATTCAATATAATGTTGCGAATACA\n+AGAAGTGCCAAGAACTACAGATAGAGAGCTTCAGGCCGTGTTTCTCTTCGTCAAAGGAAG\n+ACACATCGATTTCATAAACAGAACTTATCATGGAATTAGAAATTTGTTAACAATATGCTG\n+AAGAAGAAAATTTCACTCTATTGACAAAGGCAAATAGGATGATGTCAGGGTAGAGAAAGT\n+GAATTATTGTCAAGTGACTTATCATTGAAAATGGTAAAAGCGTAATTAAACGTTTCAGTC\n+GTGTTCAGACTACTAGCATTATGGGAAGATTTAATATTAT\n+>Kpha\n+ATGTCTACCGCC------AGTGTAGTTGAGCAACTGGAGCTGCCCTCCAGTTGCTGGAGA\n+ACGTACTTT-------------------ACCATGAAGTTAACGTTTAGGGGGTTGCGTCT\n+TGGAGCAGAGGATTGAACCAAGTCCTTCTTTACTCTGAGGTCACTATCAATTTGGGAAGA\n+TGCAGAGTTGGTTATAAGAGTTTTGGTTGAAAGGGAGGTTGCGATCATAAATACACGATA\n+CTGCAGGTATTAACAAAGAAAGATCAGAAGTTCTGTCATTGGTGCAATTGAGATGTTTGC\n+TTCTTCGTTGAAATTCTTTGAATGAAGGCTGCAGACTATTCTCAATTCGACGGTCGGACA\n+TTTACTTTACTGGGGATCCTTAAGAGTTTCAAACAGATTT--------------------\n+-ACTCGGATTTGGCAAAAAGTTGTCAAACATATTATCCGTGGGTTCGTTGCCACGAGGTA\n+TTTACACAGTTTTAAACGGAGGTATT-ATCAACGCAAGCAAGCTTTCTACACTGTTGACA\n+GGGTTTTTGGTCATGTCTAGTATGCTACCATTATGATCTTTGGATAAATATATGTAGGAA\n+TATAAAATCCCAGAACAAACTTATCAGAGTTAAGAAAAAACTGAGGCCAAGGAAAAACAA\n+AAGTGAATTTTTGTCTATTTTGTGATTTATAACATCTCAAAACAATGATAGACCTCAAAC\n+CTCAATGAAAATTTAAGCAAATAACCACTAACGATAATTTTATGATTTTGAAAACTAGAA\n+GATACAATTGGTTCATTCTAGATAGGAGCGACATCCCTGCATTTATTTATATAGCGTTAC\n+AGTAATGAAAGCCTTTACCTGAACAATATTCGTGAAAACGGTTTATTGCAAGAATGATGG\n+AATATTATTAGAAAGAGGATAAGTAATGAAA---TAAAAAGTTTTTTACTGCACTGACAT\n+AACAGATCTTGCACATGGCTAGATTTGAAAGGATCTTAACATGAAAGTAAAA---TCGAA\n+CAAACGTATGAACAATGAATCAGAAAATAACGTA----CCAAAGAAATTAAAGCAATGGA\n+TTTTCTCATCCACTCCATCTGTATTATCTCTTCAGAAAAATAAATGAATATTGTACTCAT\n+CAAGGTAAAAAGTATGTAGATATTATGTTACGACGAAAGGCTGATCTATTACTTTGGTCA\n+ATGCCTTTGAAATTATTACAATAAATATATTTTAAGAGAGGCAACCTGTTTTTCGTACCA\n+TTTACAGCTTTCCCTGTGTGCGTCTAGTACATATGATATTTTCATCTACTTTGGGTACTT\n+CATCGTGTTCGTGTTGTGTAATTCTAATAGATTACGCTGAGAAAGTTATTAATTCAACAG\n+CATGATGAGAGAAGATATCAGACACTATGCATTGTATTGAAATATAACGTCTAGAGTTCA\n+AGAAGTTCCAAGGACAGCAGATAGAGTGCGTCAGACTGTTTTCTTATTTGTCAAAGGAAG\n+ACACTTCGATTTCATAGAGAGAATATTTCATGGAATTGGCAATTTGATGATAAGATAATG\n+AAGCTGATAATATTACATTGTTAACAAAGGCTAATAGGATGATGTTAGGGGAAAGAAGGA\n+GAATTATTATCTAGTGAATGATCATTAAAAATGGTTAAAACGTAGCTAAATATCAAACAA\n+GAATTTAGATTATTATCACTGTGGGAAGATACAATTT---\n+>Kbla\n+ATGTCTTCTATTACGGAATCATCACAAGTAAT----------------------------\n+----AGTCTCTACAA-------------AATATGAAGAAGAGGTTTATGCAGTTTCCTCC\n+TAGAACAAAGATGTAAGTCAGGTTGTTCTTTATAGTGAATTGGTTTACTACATTGGGAAG\n+GGCTAAACTAGTGATTGAACTGTTGATGTAAAGGTCGACTACTGTCGTAAATTTATCGAT\n+A-AATCAATTTAGACCAAAGTAATCAATCATCTTGTTTTTGATCCAATTAAGATGTTAGA\n+TATCATACAGAAGAGACTTTAAATAAATCTACACATTACTTTTAATGAGAAGGTCATTGT\n+TAGGTTATATTGGGGATCTTGAAGAATCGAT'..b'AACGTTGGGCGCTG\n+CGGCGTTTAAGCGTTGTGTTCGCATAATAAATTGTCCCGAGAAAATTATCAATTCAACTG\n+CGTAATGGGAAAGGATATAAGACCCCCAGCGTCCTAATTAGGTACAATTCGGAGAATCCA\n+GGAAGTTCCAAGAACTGTTGACAGATGGCATCAGGCAGTGTTCTTGTTTGTGCAAGGAAC\n+ACACCTTAATTTCATAAACAGAATTTGGAATGGAACTGGAAATTTGCTTTCAAGAAGATG\n+AACAAGAAAATTCCACCTTATTAAGAAAGGCGAATAGGATGATGTTAGGGTAGAGAGAGT\n+GATCTACTATCAAGCGATTGATCATTAAAGATGGTTAAAAAGAAGCTAAATGTCTCGCAC\n+GTTGTGAGATTATTGTCACTTTGGGAAGTTTCCAATGGCA\n+>Smik\n+ATGGACGAGCTACTGGGAGATGCACTGAAGAAAACAATCAAGCAGCGAGGGCGTTGTCGA\n+-------------------TCAGAAAGATTGTCACACCCGAGGTGTTGACCATATCTTCA\n+TGGAACAACGGTCTGAATCTGTATGTTTTATACAAAGAATTGGTGGGCAACTTAGGTAAG\n+AGCGGCGTCTGTAATTAGCATGTTAGTGGCTTGGGAGATTGGTGGCGAAACTGGTGGAAA\n+A-GATGGAATGGACGTAGCAGTACCAGACCCACTGTGATTAACGCAATTGAGATGTTCAG\n+TACTTGCAAGAACGGCGATATCCGAAGAAGCAAAACTATTCATAACGGGAAGGAATCATC\n+TTTGCTCTACAGGGGATTATTATGAATTATTAGCCAAATG-------CGTGTTGGTATAA\n+GCTAAGCAGATGGTGGTGAATTGTGGAACGTTATATCATTAGGCTCCTTGCCGGGAATTA\n+TTTAAGCAGTGTCACACAGTTCCACA-GTCACCACTCATCATTATTTTGCATTGTGGAAT\n+GGGTATCTGATAATATCTAATGCTTTCCCATCGAGATCTGTGGCGTTCTATATGCAACAT\n+TACAGCTTTCCTGAAATCCCGCATCTGATTTGAGAAGGGTCTCAAGCAAAAATGAATCAA\n+AAACTGTTTTGCTAAATAATAATAAACCATGAACTTTCACAACCACAATTGATCGAAGAC\n+TTCATTAAGGATTTAAACCTCAGATCCTTGACAAAAATTTGATGGTTCAGAAGGGCAGAA\n+GTTACAATTGACTAATGCCAGGAGGGCGCTCAGTGACAGCTCAGGTTTACAATGCATTAA\n+GGCCAAGAGCAACTCCTAGCATATAGCACTCACTCAAACAGACTTTTACAAGAAGGAGGT\n+AAATCCTTTCAGATGAATTAGACTGTCGAGGAAGATCCAACTTTTTTAATGCTTTGACTT\n+GGCCGACCATTCCACTGAATGGATTTGCGTGGCAGTTGATAACAGGAAGCCATCAAATAA\n+TAAAAAACGTTCTAGTCCAAACGCTGTTACACCTTTGCGGTAAAAAATTGAAACAGCGGA\n+TTTTGTCTGCGTTACCTGCTGCTATAACTAATCCCTCCAAGGAGCGAATACACACAAGAA\n+GAAGACAAAC----AGATGATCTAACGCAGTACTGAAACCCTCACCGGCCTCTTTGATAA\n+ATATCTTTAAAACTCTTATCATAAATTCCTTCTAAGTGAAACCACCTGTTTATTGTTCCA\n+TATAGTACTATGCCGGCGTAAAACATCCGTTTATGAGATATTCTTCAACGTTGGGGACTG\n+CCGCGTTTAAGCGTTGCATTCGCATAATAAATTGTTCCGAAAAAATCATCAACTCAACTG\n+CGTAATGGGAAAGGATATAAGACTCCCGGCATTCTAATTCGGTACAATTCTGGGAGTCCA\n+AGAAGTTCCTAGAACTGTTGACAGATTGCATCTGGCAGTTTTCTTATTCGTGCAAGGAAC\n+GCACCTTAATTTCATAAGCAAAACCTGGAATGGAATTGGAAATCTACTCTCAAAAAGATA\n+AACAAGAAAATTCTACCTTATTAAAGAAGGCAAACAGGATGACGTTAGGGAAAAGAAAAT\n+GAATTATTATCAAGTGATTAACCATTAAAGATGGTTAAAAAGAAACTGAACGTCTTGCAC\n+GTTATGAGATTACTTTCACTTTGGGAAGTTTCCAATGGCA\n+>Scer\n+ATGGACGAGTTACTGGGAGAAGCGCTTAGGCAGAGAACCAAACAGTGAGAGCACTGTCGA\n+-------------------TCTGAGAAGTTGTCACCCCCGAAGTGTTGACCATATCATCC\n+TGGAACAGAGACTTGAATCCGTTTGTTCTTTACAAAGAGTTGGTGGGCAATCTGGGTAAG\n+AGCAGCTTCTGTAATTGGGATGTTGGTGGCTGGGCAGATTGGTGGCGCAGTTAGTGGAAA\n+A-GATGGTATGGATGTAGCAGCGTCAGACGCACTATCATTAACTCAATTAAGGTGTTTAG\n+TACCTGCAAGAACAGCAATATCCGAAAAAACGATATTATTCATAACGGGAAGGGAACACA\n+TTTACTCTACAGGGGATTATTACGAATTATTACGCAAATG-------CGTGTAAACACAA\n+GCTAAACAGCTGGTGGTGAATTGTAAAACGTTATATCATTAGGGTCCTTACAGGGAATTA\n+TCTAAGTAGTGTCACGCAGTTCCATG-GTCACCATTCATCACTATTCTGCACTGTGGAAT\n+GGATATCTTATAATATCAAATGCTTTCCCATCGAGATCTCTGGCATTTTATATGAAACAT\n+TACAAATTTCCCGAAACCCCGTGTCCGATTTGAGAAAGATCCCAAGCCAAGATGAATCGA\n+AAACTGTTTTGCCAAATCATAATAAACCATGAGCTTTCACAACTACGGTTGATCAAAGAC\n+CTCATTGAGGATTTTAACCTCAGCTCTCTGACGATAATTTGATGATTTAGAAAGGTAGAA\n+GTTACAATTGATTAACGCCAAGAAGGCGCTCCGTCACAGCTCAAGTTTACAATGCATTAA\n+GACCAAGAGCAGCTCCTAAAATAGAGTACTAACTCAAACTGGCTTTTACAAGAGGGAAGA\n+AAATCGTTTCAAACGAAGCCGACTGTTGAGGAAGAACCAGCTTCTTTAATGCTTTGACTT\n+GGCAGACTCTCCCGCAGAATGGACTTGCGTGGAAGCTATTATTAGAAAGCCCTCTGACAA\n+TAAAAAGCGTTCTGGCTCAAACGCTGCTGCATCATTACAGTAAAAAATTAAAACAATGGA\n+TTTTGCCGGCGCTACCTGCTGCTGTTTCCAATCTCTTCAAGAAGTGGATACACAGAA---\n+GAAGACAAAG----GGAGGATTTGATGCAGCACTGAGATCCTCACCAGCTTCTTTGATAA\n+ATATCTTTAAAAATCCTATCATAAATTCCTTTTGAACGAAACCACCTGTTTACTGTTCCA\n+TATAGCACTATGCCAGTATAAAGCATCTGTTTATGAGATTTCCGTCTACGTTGGGACCAG\n+CAGCGTTTAAGCGTTGTATTCGTATAACAAGCTGTGCTGAGAAAATTATCAACTCAACTG\n+CGTAATGGGAAAGGATATAAGACTCATAGCATTTTAATTAGATACAATTCTGGGAATCCA\n+GGAAGTTCCAAGAACAGCCGATAGATAGCATCAGGCAGTTTTTTTGTTTGTGCAAAGAAC\n+GCACCTTAATTTCATAGACAAAACTTGGAATGGAATTGGAAATTTACTTTTAAGAGAATA\n+AGCAAGAAAACTCTACATTATTAAAAAAGGCAAATAGGATGATGTTAAGGAAGAGAGAAC\n+GAACTACTATCAAGCGATTGATCATTAAAGATGGTCAAAAAGAAGCTAAATGTTTCGCTC\n+GTTATGAGGTTGCTATCGCTTTGGGAAGTTTCCAATGGCA\n' |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit Mon Mar 28 16:23:18 2022 +0000 |
| b |
| b'@@ -0,0 +1,204 @@\n+>Kpol\n+ATGTTGGAAA---------GTTAAACGTGTTCAACAATAGTTCGTTATCCATCAATTCCA\n+CAAC--AACTTGATAACGTTTCTAATTGTTTTAAAGTTTAGCTGGTCTCGTTCTACAAGA\n+TGGGTCTCCCATTGTTATCAAGATTTAACTTCCAAACACTACGATAAGTGCTTTGAGTCG\n+TAAGAGAACTGAATTATAGGTGGTAACAAGTCTACGTTTGAATATATCACTTTATCTGCT\n+ATTTCTTGAAGATCTACCATACTACTCAACTTTAGTATGTTTATTAAACTTTTTCAGACC\n+TCGAATTACCAGAACTGTTATTCCTGGCTAAACTGACCTAGCCGTAGCTGAAACATCACT\n+ACAAAAGGCTGAAGATTTGCTATACAACATCCTTTCGATCTGGCTAGGTAACCTGTTTAT\n+TGATTTTAAACGTTTCTTTGGAAATATTAAGTCTTTGCTGCAAATCTACACCAAGAAAAT\n+ATTAGATTGTTGGAAGGTATCAATAAGCTCTTGGAATTCTCAATGACTCATGTTAACTCC\n+TGCCAACTGGTTCCCTTAGTTTCTAAGGCTGAACAAGACTTTTGTTG---GCTAGATCAG\n+AAAAGAAGGTGAAAGTTCAGCTTTGCCATTCCAGTAAGAAGAAAGCTTGCCGATACGAAT\n+TTTATCTGTACTACTTTGATCTATCTAACTACCACCTTTATCGATTCCGCTATAGATAAA\n+TACTCTGATATT-GTTTGTTCTCTTTGTACGTAAGGTTCTATGCTGAGTTATTTCTCAAA\n+TTTAAAAGTTTATCTGAATTAAGAGGACACTGATATTTCTGTTCTAAAGATGACTCCGCG\n+CTAACTTTAGAATGAACAAAATGCCGAACGTCGAATGAATGGATTCTGTAAAATCCTTAA\n+ATTACCAAATTCAGTTACTCGCTGTCGGGATCCCAAATTGCCTATTTAACCATTG\n+>Kpha\n+ATGCTACCTC---------ACTACAGTTTCAAAACAATGATTAGACTGCAATAGTCGCCA\n+AACAGTAATACGAAGAATTATCCTTCTATATTAAAGTGAGGCTGGACTCGTTCTTCAAGA\n+TGGGTTTCTCATTACTTTCGAGGTTCAACTTTCAAACACTACAATAAATGCTTTGAGTAG\n+TAAGGGAACTGAACTTTAGGTGGTGATGAATCCACGTCCGGATTTATCACTTTGAAGGCA\n+GTTTTTTGGAGATTTGCCTTATTATTCGAAAATCGTACGTCTTTCAAACATTTTCAAACC\n+ATGAACTAGTCGAACAGTATTACCTGGCTCATCTGATTTAACTCTAAATAATATTCACCA\n+ACATAAAGCCGAAGATTCGCTATACAATTTGCTTTCGATCAGGTTAGGTAACCAGTCTTT\n+CGATTTGAAAGATTTCTTTGGATAGTTAAAAGCTTCGCTATAAATTTACACTAGGAAAAT\n+ATTACATCGAAGCGAGGAATTGAAAAAATCTTGAAATTCTCACTGAATCTGCATAATTCT\n+TGCCAGCTGGTTCCAATAAAGGCAGAAAACCAATCACCAT---ACTGCAATCGAGGTAAG\n+ACACGTCGGTGAATGTTCAGCTTTGCTATCCCATTGAATTAACGAATACCAACTTCCAAT\n+ATTAAAGATATTACCAAGATGTCTCTGGATACAGATTTGATCACCACTATTGTGGATGCT\n+TACTCCGATGTG-GTTTATTCTCTTTGTACGTCAAGTCATACACTATAAAGTCGGCTCCA\n+TTCAGAAATCTTTCTGAATTGAAAAGGTATCAATATCTCTTCTCTAAATATCACTATGCA\n+GCATCCTTACAGC----------------GCAACTGTGTGTTCAAAAGTTAAAGATTCAA\n+GTTGACTATTTTAATTACCGGCTGTAGGGATTCCAAATTACCTACTACATGATTA\n+>Kbla\n+ATGTTAGATT---------GAAATCAAGTTAGCCCAAATGCTTTCTATATGTGTCTGCTG\n+TTGT--ACTCAAGTGCAGTTTCTCCTTAGTTCAGAGTCCGGGTGGTCAAGATCTGATGGA\n+TGGGTTTCTCATTGTTATCTAGATTTAATTACCAGATACCGTGAAAAACTCTCTAAGTAG\n+TAAGAGAACTGAATTGTGGGTGGTAAACAATCTACGTCTGAATATATCACTTTATCTGCT\n+CATTCTTGAAGATTTACCTTATTTTTCGAATATTGCATGTTTATTAAACTTATTCAATAA\n+AGGAATTAACAGAACTGTCTTACCAGGCTCAACTGATTTCCAAGTCTCTCTTTTAGACCT\n+GTAGACTGCTGAAAATGGGTTATTCAACCTTCTTTCGAAACGGTTGGGTAACCAGTCTAT\n+TGACTTAAGAAATCAATGTTGATATATTAAAACTTCTCTCAAAGTATATACAAGGAAAAT\n+ATTGAATCGTTGGAGGCCGTCAATAAGCCCTTGAAATTCTAGAAGAATCAGAATCCTCAA\n+TGCCAACAGGTACACTTGGCTAGCTCTCAACCACAAGACTTTCAGTG---GCCAGATTAG\n+ATCTTTGGGTGAACGTCGTGGTTTAGTGTACCTGTCAGAAAAACAATCGATGATTTGAAT\n+CTTGGCCACATTGAATTCCATTAAGTTCAATATAAAACTGTTGATGATTGTATACTAAGA\n+TTCAATGATATT-GTCTCTTTACATTATATGTCAGGAACTATCCAGCTCAATAGGTACTA\n+TTCAGCTATTTCAATCAATTAAAAAGGCCAAGATATCACCAAGCAATTGATAACCGAAGT\n+GTTTCGATTGAATGCCTCTGTTGCAAATGAAACAATGGTCTTCCAAGATAAAGGAATCAA\n+ATTGAACGATTCAGTTACTTGCCGTTGGAATTCCAAATTGCCTTCAAAATGATTA\n+>Sdai\n+ATGTTGCATTACAAAACTTAAATTTGCTAGAGTCTCTTTAAACATTACATGTCTTAGCTG\n+TGGT--AGCCAAGTAAAGTTTCCCATTAGATGAAAGTCCAGCAGGGCCAGATCGAATAGA\n+TGGCTATCTCACTATTATCTCGCTTCAATTTCCAAATACAATGATAAATGCTTTACGTAG\n+TTAGAGAACTGAATTGTAAGTGGTAAAGCTTCCACGTTTGAATATATTACTTTGAAAGCT\n+ACTTTTTAGACATTTACCATATTATTTAATCTTACAATGTCTATTAAACATTTTTAGACC\n+TTGAATTACCTGAGCTGTTCTTCCTGGCAAACTCGACCTGGCACGTTATGACCAAAATCT\n+ATATGTAGCTCATGAATTATTATACAATATTCTTATGATCTGGATAGGTAACCAATTCTT\n+TGATTTAACCTATCGCATTGGAGAAATTCAAATTTTGCTGTGATTTTATACGAAGACAAT\n+ATTGTATAATTGGTCGGTGTTAACCTAACTCTTAGGTTCTTAATGATTCTTATTTATTCA\n+TACCAGTTGGTAAACTTAGTTGGATCAAGCGCAATAATCTTTCGTAGAAAGCAAGATAAG\n+AAATGTAGGTCCACGTATAACTTCGGTATTCCAATTGCGCTAGGATTTGGTAATATTATC\n+TTTATCCAAATTACCGTAAGAGCACCCCATACTAACTTGGTATCTTCATCCAGTGATTTC\n+TATAATAATAAGAGGTTGTTCATATTGAATGTCTTGCAGTATCCAGAAATATTAATAATG\n+CTCAGAACTTTTACCGAATTGAGAAAATATTGATCTTTCAGTGCAAAAGAACGCTGTAGA\n+TTAGAATTAGAATCAATTTAAATTGAAACTTGGAAACGTTCGGAAAGGTTAAAAACTCAA\n+ATTGGACAGTTCAACTACCTGCTGTGGGGATACGAAATTACCTTCTTGATGATTG\n+>Sca'..b'TAAGTTGCCTTCCGTATCATTG\n+>Suva\n+ATGTTGCTAG---------GTTGCAATTGCCCAGGGGTAGTTAGATTGCTGTGTCAGCCA\n+GAGC--GCTCCAGTAAAGTGTCCCTTTGGCTCAAGGTCCAGGTGGGCTCGTTCAACCGGA\n+CGGGTAGCTCACTCTTGAACAGGTTCAACTTCCAAACACAATGCCAGGTGCGTTGAGTGG\n+TCAGAGAACCGAATTATAGGGGGATTTAAGTCCACTTGCGGATATATCACTCTAAAAGCC\n+ACTTCTTGGTGACCTTCCTTACTACTCAATCCTGCAGTGGTTGTCAAACTGCTTCAAGCC\n+CCGAGCTACCTGAACTGTTTTGCCTGGCCAGATCGATTATGCTGTTGCTGAGCAGTGCCC\n+GAAAAATGCAGAGGAACAGTTGTTCGCTATTCATTCGAAAGGGCTGGGAAACCATTGCCT\n+CGACCTGAAAGGTCAGCTTGCAAATATCAAGGTTACGCTGCAAATCTACACTAAGAGAAT\n+CTTGAATCACAGGGAAATATCGTTAGGCCTTTGAGATTCTTGACGATTCCTGTTGCCACT\n+TACCCACAGGCAAACACGGTAAGTAAATCCGAACAAATCCTTCTTAGGAAAACAGACAAG\n+ATTCCTCGGTGATCGTTCTGCCTCAGTATCCCTGTGACAAACATCTCAGCCCATACGAAT\n+CTTGGCCGCATTGCCTCGCGCTTTCCGATCCCCGGCTTGGTCAACACTGCCACACAAAAA\n+TTCAGTGACGGC-GTCTCTTCACTTTGACCGTCGAATCAAACAGCTCTGTGTGTCCGCAA\n+CTCAGAGATTTTGCAGACTTGAGAGGGTAAGGATTTATCACCTCGGTAATACACCATGAG\n+AATGCTGTACAATGAACATGTTTTCAACGGCCGAATGAACCGACGGCGTGAAAGACTCAA\n+GCTAGGTAGTTTAACTACTAGCTGTTGGAATTCAAACTTGCCTATTTGATGATTG\n+>Skud\n+ATGTTGCTAG---------GTTGCAATTGCCCAGGGGTAGTGCGGTTGCGGTTTCAGCCA\n+GAGC--GCCCCAGTAAAGTGTCTCCTTGGGTCAAGGTCCAGGCGGGCCCGTTCAACCGGA\n+TGGGTGGCCCACTTTTGAACAGGTTCAACTTCCAAACACCACACCAGACGCCTTGAATGG\n+TGAGAGAACCGAATTATAGGGGGGTCCAAGTCCACTTACGGATACATCACCTTGAAGGCC\n+ACTTCTTGGCGACCTTCCCTATTACTCAATCCTCCAGCGGTTGTCAAACTGATTCAAGCC\n+TCGAACTAACTGAACTGTTTTGCCCGGCTAGATCGATTATGCGGTTGCTGAACAATGTCC\n+GAAAAGCGCCGAAGAACAGTTGTACGCCATCCATTCGAAGGGGTTGGGAAACCACTGTGT\n+TGACTTGAAGAGTCAGCCTGCAAATATCAAGGCTACGCGGCAAATGTACACGAGGAGAAC\n+CTCGGGTTACTGGGAAACATTGTGAGGCCCCTGAGATTTTTGACGACTCATGCTGGCACT\n+TACCTGCAGGCGAGCGTGGCGGGTAAGTCCGAACAAAGCTTTCCTGGGAGAATAGAGGAG\n+ATTCATCGGCGACCGTTCCGCTTTGGTATCCCCGTGACAAGCGTCGCAGCCCATACGAAT\n+CCTGGCCGCATTGCCTTGCGCTGTCCGATCTCCGGTCTGGTCAGCTCCGCTGCTGATAAA\n+TTCCGCGACGGC-GTCTATTCACGCTGCTTGTCGAATCAAACAGCGCCGTATGTCTGCCA\n+CTCAGAGATCTTGCCGATTTGAGAGGGCACGGACTTGACTCCTCCGTAACACTCTATGAG\n+AATGCCGTCCAATGAAGCTGTTTTCCATCATTGAACGAATCGACGGCGTGAAGGACTTAA\n+GCTGAGCAATTCAACTACTGGCCGTCGGGACTCCAACTTGCCTATCTGAAGATTG\n+>Smik\n+ATGTTGCTAG---------GTTTCAATTGCTCAGGGGTAGTTAGACTACTGTTTCAGCAA\n+GAGC--GCTCCAGTAAAGTGTCTCGTTGGCTGAAGGTTCAGGTGGGCTCGTTCATCCGGA\n+TGGGTGTCCCACTTTTAAGCAGATTCAACTTCCAAATACAACAATAGAGGCCTTGAATGG\n+TCAGAGAACCGAACTATAGGGGGACTTAATTCAACTTGTGGATATATCACCTTGAAAGCT\n+ATTTTTTGACGACCTTCCCTACTATTTAATCATACAGTGATTGTTAAACTGCTTTAAACC\n+TCGAGCTAACAGAACAGTTTTACCTGGCCAAATCGATTACGCGGTTGCTGAACAATGCCG\n+GAAAAGCGCAGAAGAACAGTTGTACGCCATTCATTCGAAAAGGTTGGGGAACCATTATGT\n+CGATCTGAAAAGTTAGTTTGCAAATATTAAGGCTTTGCGGCAAATGTACACCAGGAGAAC\n+TTGGAGTTAGTGGGAAACATCGTTAGGCCCTTGGGATTTTTGACGATTCATGTTAGCACT\n+TACCTGCAGGTAAGCGTGGTGAGCAAATCTGAATAAATCCTTTGTAGGAAAATAGAGGAG\n+ATTTATCGGTGACCGTCCGGCTTTGGTGTCCCAGTGACAAGCTTCTTAGCACATACGAAT\n+GTTGGCCACACTGCATGGCACTCTCTGATCTCTGGTTTGGTCAGCTCCGCTACTGATAAG\n+TTCAGTGACGGT-GCCTGTTCACTTTAATTGTTGAATCAAACAGCGCTGTGTGTCTGCTA\n+TTCAGAGATTTTGCCGGTTTGAGAGGCTACCGACCTGTCTCCTCTGTAATACACTATGAA\n+AATGCTGTCCAGTGGAGCTCTTTCCAGTCGTTGAACAAATCGACGGCGTGAAGGACTTAA\n+GTTGGGTAATTCAACTACTAGCCGTTGGGATTCAAACTTGCCTATTTGACGATTG\n+>Scer\n+ATGTTGCAAG---------GTTGCAATTGCCCAGGGGTAGTTAGGTTGCCGTTTCCGCTA\n+GAGC--GCACTACTAAAATATCTCATTGGTTTAAGGTCCAGGAGGGCTCGTTCAACCGGA\n+TGGGTGGCCCACTTTTAAACAGATTCAACTTTCAAACACGACACTAGAAGCTTTGAATAG\n+TCAGAGAACCGAATTATAGGGGGACTTAAGTCTACTTGTGGATACATCACTTTGAAAGCT\n+ACTTTTTGGCGACCTTCCCTACTACTCAATCCTACAGCGGCTATCAAACTGCTTCAAACC\n+TCGAGCTCACCGAACTGTTTTGCCTGGCTAGATCGATTATGCGGTCGCTGAACAATGTCG\n+GAAGAGCGCCGAAGACCAATTGTATGCCATTCATTCGAAAGGGTTAGGAAACCATTGTAT\n+CGATTTGAAGAGTCAGTTTGCAAATATCAAGGCTTTGCGGCAAATCTATACCAGGAGAAC\n+CTTGAGTTAGCGGGAAATGTTGTTAGGCCTTTGAGATTTTTGACGAGTCACGTTAGCACT\n+TGCCTGCAGGTAAGCATGGTGAGTAAATCCGAACAAATTCTTTTTGGGAAAACAGGGAAG\n+GTTTATCGGTGACCGTTCCGCCTTGGTATCCCGGTAACAAACCTCCCAGCTCATATGAAT\n+ATTGGCCACATTGCCTTGCCCTATCCGAGCTCCGGTTTAATCAGCTCGGCTACTGATAAA\n+TTCACTGACGGC-GCCTATTTACTCTGTTTGTAGAACCAGACAGCGCCGTGTATCTTCCA\n+CTCAGAAATTTTGCGGATTTGAGAGGGCAAGGACTTATCCCCTCAATAATACACAATAAG\n+AATGCCGTCCAATGAATCTGTTTCCAGCCATTGAACAATTTGACGCCGTGAAGGACTTAA\n+GTTGGGAAATTCAACTATTAGCCGTCGGGATTCCAACTTGCCTATTTGACGATTG\n' |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(Kpol:0.2117200757,(Kpha:0.3473730087,(Snag:0.3909327952,(Suva:0.0946872844,(Skud:0.0889121326,(Smik:0.1049059674,Scer:0.0949313553):0.0232511757):0.0453962230):0.2425218885):0.0870775929):0.0584804305,((Kbla:0.3238803175,Kafr:0.3460885972):0.1134493453,((Sdai:0.2347934241,Scas:0.3009185406):0.1557663256,Cgla:0.3139365522):0.0477467321):0.0796422841); |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/Steenwyk_etal_mBio_2019_EOG091N44MS.aln.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Steenwyk_etal_mBio_2019_EOG091N44MS.aln.fa Mon Mar 28 16:23:18 2022 +0000 |
| b |
| b'@@ -0,0 +1,1080 @@\n+>Aspergillus_aculeatus\n+atggccgacatcctaacccaactccaaacctgcctcgaccaactagcaacccaattctac\n+gcaaccctaggctacctaacaacctaccacgataacagccccgccacccccccaccaacc\n+accgcgcccgccgcgcccgcgctcgccaaaatccccaagaactcctccgcgcccccggtc\n+cccgccagcgcgcccctcgccgcccagcagagcaaccaaacccaacaacaaacacccgcc\n+gagccacaaccagcacaaccaggcgcggccgaagacaca---------------------\n+---------acaggcacagcccaagaccccgccctcccgccggcgcccgactcgccccgg\n+acgttcgcggcgcggcagcgcgagctggcccgggatctggtgctcaaggagcagcagatc\n+gagtatttgattagtgtgctgccggggattgggtcgagtgaggcggagcaggagcaccgc\n+atccgggagctggagggggagttgaggcggtgggagggggtgaggggggagaggatgctg\n+cagctcaaggcgttgagggggcggttggagggggtgttgggggcgatggaggtggggata\n+tatggggagcgggaggtt------\n+>Aspergillus_arachidicola\n+atggcagacattctaacgcagctccaaacctgtctcgatcaactcgcaacccaattctac\n+gccacaataggctacctcgtaacctatcacgataattcacccgcaatcccaccccaaaat\n+gaccccactgccgcgcctgccctcgccaaaatcaccaagaactcgaccgcgccgcccgtc\n+cccgctggtgcgcct---------------------gcaggctcccaagcatccccacaa\n+caacaatcggctcaaatcccaggccaacagcagcaaggaggtggtgatgcaggacagaca\n+cccggagctggagggacgggcgccgacccgaatctaccgcctgcgccggattcgccgcgg\n+acgtttgcgagtcggcagcgggagttggcgagggatttggtcatcaaagagcagcagatt\n+gagtatctgatctcggtacttcctggaattgactcgtcggaggcggagcaggagaggagg\n+ataaaagagttggagaaggagctgagaagcgcggaggaggacagggaacaaagagtgcgg\n+gaattgaggaagttgcgaaagaagctggagaatgttttaggagctgttgaggtgggaatc\n+tatggagatcgcggggttgtggcg\n+>Aspergillus_awamori\n+atggcagacatcctcacgcaactccaaacctgcctggaccagctcgcaacccaattctac\n+gcaaccctctgctacctcacaacctaccacgacaacatccccgcgacgccacccccgaca\n+acgccgagcgccgcacccctcctcgcaaaaatccccaagaacgcatcaacacccccggtg\n+cccgcgtccgcgccccaagcagca---------caatcccaatcgcaagcgtcgccgcca\n+ccacccgacagcaccaaccccccgggccagggaccgaatgcagacaaccagcaacaaaac\n+gcagatggg------------acagcagaagggtta---cctgcgccggatagtcccgct\n+acgtttgctgcgcggcagagggagttggcgcgggacctggtgattaaggagcagcagatc\n+gaatacttgattagtgtgttgcccgggatagatagtagtgaggcggagcaggagagaagg\n+attcgggaactggagggggagttgagggttgtggagggggtgagggaggagaggaggagg\n+gagttgggggtgttgaggaagaggttggagggggttttgggggtggtggagagggggatt\n+tattctaggggt------------\n+>Aspergillus_bombycis\n+atggcagacattctaacgcagcttcaaacctgtctcgaccaactcgcaacccaattctac\n+gccacattaggttatctcgtaacctatcatgataattcacccacaatccccccccaaaat\n+gatcccactgctgcgcccgccctcgccaaaatcaccaagaactcgagcgcgccgcccgtc\n+cccgccggcgcgcct---------------------gctgcctcccaagcatccccacaa\n+caacaagcggcccaaatcccaggccaacagcagcaaggaggcggtgatgcaggtcagaca\n+cccggagctggagggatggccgccgacccgaatctgccgcctgcgccagattcaccgcgg\n+acatttgcaagtcggcagcgcgaattggcgagggatttggtgatcaaagagcagcagatt\n+gagtatttgatctcggtacttccaggaatcgactcgtcagaggcggaacaggagaggaag\n+attagggagctggagaaggaactgaggagtgccgaggaggacagggaacagagagttcgg\n+gaattgaggaagttgcgaaagaagctggagaatgttttgggggctattgaggtggggatt\n+tatggggatcgtggcatcgtggcg\n+>Aspergillus_brasiliensis\n+atggcagacatcctaacccaactccaaacctgcctcgaccagctagccacccaattctac\n+gcaaccctctgctacctaacaacctaccacgacaacatccccgcgacgcctcccccaaca\n+acacccaacgccgcgcctctactggcaaaaatccccaagaacgcatccacacccccgaac\n+cca---------------------------------------------------------\n+------------------------------------------------------------\n+---gatggg------acgggagcggcggagggactagcacctgcgccggacagcccggcg\n+acatttgcggcacgacagagggagctggcgcgggatttggtcatcaaggagcagcagatt\n+gagtacttgattagtgtgttgcccgggatagatagtagtgaggcggagcaagagagacgg\n+attcgggagctggagggggagttgagggttgtggagggggtgagggaggagaggagacgc\n+gagttgggggcgttgaggaggaggttggagggtgttttgggggtggtggagagggggatt\n+tattcgaggtct------------\n+>Aspergillus_calidoustus\n+atggcggacattctaacccaactccaaacatgccttgaccagctcgcaacccaattctat\n+gccacaatcggctacctaacaacataccacgacaactcccctgcgacagtcccggaccat\n+---ccaaccgcagcgcccgcactcgcaaagatccaaaagaactccacaaacccacctatc\n+cccgccagcgcagccgcgatcctc------------gcaaactcgcaagcatcaccatcc\n+---------------------ggcgcaggcgctacaacgccggggcctatagcaactgtt\n+ccagga---acgggaacgggggaggacccgacgctcccgccgcgcccggactcgccgagg\n+acgtttgcggcgaggcagcgcgagcttgcgcgtgatttagttatcaaggagcagcagatt\n+gagtatcttgtctcggtgctgcctgggacggggtcttcggaggcggagcaggaggggagg\n+attcgagctcttgagaaggagttgaggggggcggaggagcagagggctaagcgggttagg\n+gagctgagggctttgagaaggagggttgaaggggtgttaggg'..b'um_verrucosum\n+atggctgacatcctcacgcagctccagacttgcctggatcagcttgcaacacaattctac\n+gcaacacttggttatctcacaacataccacgacaatgcccccacaacaccaccaccaaat\n+gtccccgacgcagcaccagccctagcaaagatcaccaagaactcatcatcaccaccagtc\n+ccagcagccatcgcaaataaagtgggtgcagctgctgttgcgggcaatgcatcaccccca\n+caggcgcctcctcaacaacccggagctgcg------------------------------\n+ccagggagagcagtagaaggtgaagatcccaaccttcctcccgcgccagactcgcccagc\n+acatttgcaagccggcagcgggagcttgcgcgcgatctcattatcaaagaacagcagatc\n+gagtaccttatctccgtgcttcccgggattggcgcctctgaggctgaacaagaaaccaga\n+atccaggacctggaaaccgagcttagaggcgtcgagaaggagcgcgctgcgaaagtgcgg\n+gagttgaaaaagttgaggactcggttggaggatgttcttggcgctgtcgctgtgggtatc\n+cacggggatggttactctcaaaac\n+>Penicillium_vulpinum\n+atggctgacatccttacgcagctccagacttgcctggatcagctcgcaacacaattctac\n+gcaacacttggctatctcacaacataccacgacaatgcccccacgataccaccgccgaat\n+gtacccgatgcagtaccggccctagccaagatgaccaagaactcatcatcaccaccggtc\n+ccagcagcgatcgcaaacagagtgggtgcagccaccgttgcaggaaatgcatcaccaccg\n+cttgcgcctcctcaacaacctggcgctgcg------------------------------\n+ccagcagcagcagcagaaggtggagatcctaacctccctcctgcaccggactcacccagc\n+acatttgcgagtcggcagcgggagcttgcgcgcgatctcattatcaaggaacagcagatt\n+gagtatctcatctctgtgcttcctgggattggcgcttctgaggctgagcaagaggctaga\n+atccgggaactagagacggaactcagagacgttgaaaaggagcgcgccgcgaaagtccgg\n+gagttgaagaagttgaggaatcggctggatgatgttctcggcgctgtggctgtgggtatc\n+catggggatgggtatcctccaaag\n+>Trichoderma_reesei\n+atgggcgaccgactcacgcagctacaagatgcagttgatcagttcgctcagcagcttgtc\n+gcttgcatgcactttgtccagatgcgccatgatctcgagaaactaggtccaaacgacaag\n+atccgcgagcctaag---------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------------gagcaagcggcaaaagaagtggatgccctgcct------ccacaa\n+gactttcgagccggcctagtcgagctttcgcgagacctcattgtgaaggagcagcagatc\n+gaagtcctcatctcaacccttcccggcctcgacaacagcgaacaagaccaggagcgacac\n+ataagggaccttgaagaagacttgaagacggccgaggcacagcgggtggaagcactgagg\n+gagaaggagctcatcttgacccagcttgacgccatcatacgcaacgtacggcggcca---\n+------------------------\n+>Trichophyton_rubrum\n+atggcggatatcctcacgcagctccaaacatgccttgatcagttggcgacccagttctac\n+gctactctctgctatctcactacctaccatgaccattcgccagccatacctccaccaaac\n+gtcccaaccgcaatcccgcagctgaagaaaataccaaagaacgca---ccgccaaacact\n+ccagccgctcagccggcctcggga---------caagcgcaaggacaagacactccccag\n+cagcaacagcagcagcagcagcagcagcaa------------------------------\n+ggagaggccggaacgcaagagcagaacaaggatcttccaccacggcctgattcgtcgaac\n+acatttgcccagcgacagagagaattggcgagagatctaattataaaagagcagcagatc\n+gaatatctcattagcgtgcttcctggcatagggagcagtgaggcagagcaagaagccagg\n+atacggcagctcgcagatgagttacgggaggcggaaaagatacgcagacggaaacgaaag\n+cagatgaagaaacttgcagaaagtattgatgggctgctggaagctgttagtcgggggata\n+------------------------\n+>Uncinocarpus_reesii\n+atggcagacatcctcacccagctccaaacctgcctggaccagctcgcaacccaattctac\n+gccacaatcgcctacctcgacacctaccacgaccactcccccgccatcccaccccccaac\n+gtccccaacgccgtcccgcaactcaacaagatccccaagaatcct---cttcccgccgtc\n+gctgccgccggcacgacagccaac------------acccccggcgcgccgctgcccccc\n+------------------------------------------------------------\n+---gacgcccaacagcaacagcaacacccagacggtccgccg---cccgactcgccgggg\n+acgttcctcatgcgccagcgcgagctggcccgcgatctgatcatcaaggagcagcagatt\n+gaatatttggttagtgtgctaccggggatcaaatcgagtgaggcggagcagctggagcgc\n+atcaagcagctggcgggcgagttgagagcggtggaggaggagcggagctcgaaacgaagg\n+gagttgcggaagttgggggagaaggtggacggattactgggggcggtgagtaggggaatg\n+---ggagat---------------\n+>Xeromyces_bisporus\n+atggccgacatcctaacccaactccaaacctgtctagaccaactagcaacccaattctac\n+gcaaccctctgctacctaacaacctaccacgacaacatccccgccctcccaccccccaac\n+aaccccgatgcagctccaccacttgccaaaatcccaaaaacctccaccgcacccccggtc\n+cccgcgacggcgccacaggaagatcagaaacacggtcagcaacaatcgcaacaacaacaa\n+aatcagcaacaacagcagcagcaacagcaacagcaagaggcaaatcaa------------\n+gcaaaccaaccggaacctatagatgacccaacgataccacctgagccggactcgccgcgg\n+acgttcgcgagtcggcagcgggagcttgcgcgggatttagtgctgaaggagcagcagatt\n+gagtatcttgtgtcggtgttgcctggggttggcgcttcggaggttgagcaggagggtagg\n+attcgggagttggagggggagctccgaggggtggaggtggagaggggggtgaagatgagg\n+gagttgaggggtttgagaaggaggttggagggggttttgggagctgttgaggtggggata\n+tacggggatcggggggttgttgcg\n' |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/alignment_list_for_create_concat_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment_list_for_create_concat_matrix.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit +12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit +12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit \ No newline at end of file |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/out.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.fa Mon Mar 28 16:23:18 2022 +0000 |
| b |
| b'@@ -0,0 +1,24 @@\n+>Cgla\n+ATGTTGCT-----------GGGCCAATGTTGAGATCATTGCCCATTACGTATTGTTACTAAGGC--CTTCAGGAAATCTATCTTACTAAATTAAGGTACAGCTGGTCTCGTTCGAACAGATGGATCGCTCACTGTTGTCTAGATTTAACTTCCAAATACCATACTAAGTGCTTTGAGTGGTGAGGGAACTGAGTTGTGGGTGGCGCTAAGTCTACGTTCGGATATATTACTCTGGAGGCCCCTTCTTGAAAACCTGCCATACTATTTAATGCTACTATGTCTCTCAAACCTCTTCAGACCCTGAATTACCAGAACTGTTATTCCAGGCCAAGTCGACCTTGCTGTTGCTGATTCTAACCAACTCCAAGCCGAAGACTTACTATACAACATCCATTCGAAATGGATAGGAAACCTGTCTGTTGACTTCAAAAGTTAGCATTGATACTTGAAAGATTCTCTTCAAGTCTACACAAGGAAAATATCGAATCGAAGGGTGGTATTAATAAGCACTTAGAGTTTTCACTGAATCTCATTTACTCTTACCACAAGGATCTACCGGCTTCATCCGCCAAGATGAATTTTCACCGAAGAGCAGATAAGAAGAATCGGGGAGTGTTCTTCATAGGTATTCCAGTTCTTCAAGGATTCGGAAATTCCAACCCTTGAACTATTGGCTTGAATTGTTCCCTCACTGACCTTCTATCGGAAGTTATCACCAAATATCCAGATGTT-GTTTCTTGACCTTCAGTGTGAGACGGTATGCTACTGTTTATCTGAAACTCAGAGGTGTTGGCGAGTTGAGAATCCCAAGATATTTCCAAGCGACTGATCGCTATGAATTGGGAACTGAGCTCT---------TCTCGTAGATATAATTGATGGTGTCAAGGACTCAAACTAGACAGTTCAACTTTCAGCTGTTGGGATTCTAAGTTGCCTTCCGTATCATTGATGGATATTCTTTCTGATATAAAAGCATCGTTCAGCAAAACCCACTGCCATTAAAAGTGGGGATAGCGTTTATGACC--CAACAGACAGCACTTCTACTGAGGACTAGAGTGTAAGCTCGTGGAACAAAGATTTACACCTGGAAATTTTGTACACAGAAGTGATTGTCAATCTGGGTAGGAGCTTCCACTGTGATCTCTTTGTTAATTTTTAGGTCGATTACAGCAGAAGATATATAAATG-TTTACCATGTCCATTGCTCAATAAAAGACCCTATGCCTTACTCAACTTAGATGTTTGATACTTGGAAGACCTAAACGATCTGAAATACATATATTATTTACAATAAGACGGTGATACCTGTGCTGTATAGGAGATCATCATGACTCTCCTCTCGATTTCAGAAAA--------------AGAGGCCAATTGTGGAGGATCATAGAACATATTGTCCTTGGGATCCCTTCGCAAATCTATTTGGAAAATGTCACCACATATCCCC-ACTGAGAGTCTGGTTTATTTTGGATTATGGAATGGTTTTTTGGGGCTAACAAATTGCTTGCCATAAAGACCTATGGACCATTGTATGAAGGAATATCCAGTGCCCGAAACTACTCATCTGACCTAAAAAAGAACAGAAGCGAAAAACAAGCAAAAACCGGTTCCACATTTAATGGGGCTTCACGATTTATCGAATGATAACTAGATCTTCGACCTCTCTGAGAACTTATTCCACTGGACATTAACTACAATATCAAGATTTCGAAATCAAGGAGTCACAGCTAACAAATCCTAGATAGGAGACCAGTTTCTGCTCAATTGTACACAGCATTAAAACAAGGAAATACTCCTTATTTAACGTACTTTCAGAAACTGTTTATTACAAGAATGAGTAACGGCAATGAGTATGAGATGGACTCTAGAAAAAATACCTAGTTATTTACAGCGATGATATCTTGAAAAGTACTAAAAATTTAAGATAGAAAACAGTTAGTGTTGAGAAAAAA---TCTGGTAAAAGAAGTCAAAACCAAGAGAAATCTGCCAAC----ACTAAAAGATTAAAAAAGTGGTTTTTGTCATCATTACCAACTGATAATAATCTAGCAATGAAAAGAAATACGATGT------GAAGTAAGATGGTA----------AGGGAGTGAAATGATGCTGATCTGTTTCAATAATTAATACCCTTAAAAATATTATCATTCCTGTGTTTTGAAAGAGACTACCTGTATACTATTCCCTACTCAATTATACCGGAGTGAAACATCTATCTACGATATATCTGTCAACTCTTGGCTCATCAAAGAATTAGAGATGCATTAAAAAAACAAACTATTCAGAAAAGGTAATTAACGGTACTGCATAATGAGAAAGGACATTCGTCCCAACGGATTCTAATCAAATATAATGCTGTGAATTCAGGAAGTACCTAGAACTGTGGATAGATTGCATCGGACAGTCTTTCTATTTGTGCAATGAGCCCACATTAATTTTATAAACAAAACTTAGCATGGAATTAGAAATCTACTCACAAAAGAATTAGGATGAGAATAAAACTTTGCTGATGAAAGCAAATAGGATGATGTTAAGGAAAGGAAAGAGAACTTCTTTCCAGTGACTGATCACTAAAAATGGTCAAAACGGAACTCAACATTTCACTAGAATTCAGGCTAATGTCACTGTGGGAAGTTTTGATTTTTTATGATATGTAACAGTTGTTGAAAGAGGCCAAAGTGGATTGGCCGAGGTATTTGAAGAAGCCCGAATTGTATGAGGTTTAGTTAGACCCTGATAATACTTTGCGCGTCTTTTTAGGTAAATTTTCCATG---------ATTCCCAATTTGTATGATTCGGTGGAGCATATAAGAAAGCATTGATATCAACCCAGAGTTATTAGTTGGAAAGGTTTATTTCATATTAAAGATACCGT-ATTTCCCCAATTGGATCCTATGATATTTTACACTTTGTGCTAATATGCCGATGTTCTTGTGACAGGGAATCACAAATTAATTATCGATGATATAAAGAAAATGAGAGATTATCAGACTGAGGAACATATCTGAGACACCTAGTCAGGAAGGACTTTGAAACTGGCCACTTTTAGTTCTTCTCGCCCTTGATAATTGTAAGTTATTGAATAAGAAGGAGCAGGACCGGATTGCTCGATCAAAAGGAAAGACTCAATTTAGCACGCAGATCCTTCATTCATAAAATTAATAGTTGGCTTGGGAGGTGTATGCGTTCCGAGTGACAGATGTTTCAACTGGTTAATTTGTAGATATGATGAAAACGGCAAAATTAGAAGAAGAATTAAATACAGTAGTACTACTTCAATGCCAGCAAGAAACCTTTATATTTGAGAGTCAAACTACTTGAGTGGTCTATGATCACGTTCTAGATGTTGGAGCTTTATTTGAATGGCAAGATATAGTGATTGGATAAAATAGAACTAAAGTTATTCTCATTCTTCAGATTCCCAAATGAGCCATTACTGTGTATTGTATATGGGCTCTTCTAGTATTCTCAGTATATAAAGTGCAAATTCAAAAGTGATGACTGATGAAACACAGGCTGATGCTAAA---AGTGATGTTCAGCTTGAGTCATCGTTGCTGGATCT---GATGAAGAAGATTGAACGGAATGTGAGGTCTAATGAACACAGGG-------TATGTAGGACTAGTGGAAAGGTATACTGTTGGCAATGCTGAAATATTAAGAGCTAAACTGTATTCTGCGCAAGAATTATATGTTACTTTATTATCAGGGAATATGAATGCCCTATTTAAAGCTGGAATTCATTGAAGCGATATGTTAGCTTGGGTATCCCTTCTTTAATTAAAGAGGAATCACGATTGCGCTTGGTCTGTCTACACATAGTGGATAGCAAATATAAGTGCTTTGTCGTTATTTGATAGGTTCTGTTGAGCAACATCTAATACCGAAGCAAACTAGGAAAGTTTATCACATGGAAAAGAAACTGGACGGG'..b'GTGTTCGTATAACAAGTTATGCTGAGAAAATTATTAACTCAACTGCATGATGAGAAAGGATATAAGACGCATAGCGTTTTGATTAGATACAACTCGGGGAATCCAAGAAGTTCCAAGAACTGTTGACAGATTGCTTCAGGCAGTGTTCTTATTCGTGCAAAGAACACACCTTAATTTTATAAGCAAAATTTGGAGTGGAATTGGAAATTTGCTTTCAAGAAGATAAACAAGAAAACTCTACTTTATTAAAAAAGGCAAATAGGATGATGTTAGGGGAAAGAAAATGAGCTTTTATCAAGCGACTGATCATTGAAAATGGTCAAAAAGAAGCTGAATGTCTTGCACGTTATGAGACTCTTATCACTTTGGGAAGTTTCCAATGGCAATGTTGCGTCACAACTGTTGAAAGAAGCCAAGCTAGATTGAAAGACGGACTTGAAGAGACCATGAATATTAAGGGTCTTATTAGATCCTGACAATACTTCGCACATCTTTTTAGGCAAAGGTTCAAGTCTGTGGCAGCCAAATCGTTTGGAGAGCGCCACCGCTCATATATATCTGCTCCAAATTGGCCTGAAAACCTTTAGATGGAAGGGTCTTTTCCCTATCAAGACCACCAC-GCGTTCCAAATTACTTCGTATGATATTTTGATTTATGTGGCCATATGCCGATATTCTTTGAGCAGGCAGTCTCAAATAATCTGTAAATGACATAAAACTATTGAAGACTCATACATGCAGAAGGGCTTTTATGAGCATTTGAACTGGATTTTAGGCGACCATTTCTATTAGCTCACCACGGCGCCTTATTGATCTTTAAAATTATGTCCAATACAGAAATCACAGAAATTGGTAGGCCTACAGAATAGATTAGACTAAAAGCCGCGATCCGGATTTCATTAATTAAACTCATCTCTTGGGAAATCATTAAATTCAGAATGACAGCTGTCCCAGTTAGTAAATTTCTCACTATGATCACTAAGAGTGACACCGAAAATGAGCTGAATATAGTCATTCTAAATCTATGCCGTTAGGAAGAAGGATTTCTCATGAGTCAAGAGATTCGAGTGGTCTTTAGTCATCATCCACTCGCTGGCGAAATTTTTGAATGGAAGGATACGAAGATTGGACAACATGGATGCTACGCGATATACATATTTCAGATTTCCTAAAGATCCTTTACAATGTTCTTTATCTGGGTTTTTCAAACTTTCAAAATATATATCAAGAGCTTGGAGCCACTAACCAACCGCCTGAAAGTCACGACAAGGGAAAAACAGACAAAATACATGAACATGTAATAAGGTAAATGAAGAAAATGAAATGAAATGGCCAAGAAGTGGCCAAAAAGATGCAGAGATCCATGAAATCAGTTTATTGGAAATGAGTTGTGACTGCATTACAGAAATATCGTAGTGCAAAATATATTTTGCACACGGATTTTAGTGTATTTTACTCACCAAGAATACGAGATCTTGATTCAAAACGGGAATTCATTAATGCTATACATCAGTTGGGAGTTTATTTGCCATTAATAAAAGGCGTTTCCCTGGATCTGGCCCTGTTTATACATAGTTGATGCAAAGTATATGTGCGTTAAAATTGTACGATATATTTTATCTGCGATTTGACAATATACAAGAAAAATGGGTAAGATAATTTCATTGAAAAAGAACTGGGGGGGCGATGACTTTATTGACCGATGCATGACACTCCTGTTGGAAGTACATGGCATCGTGGAGTAAGCACTATGGTTCATGGAAGAGTTTGGTCGGCCTGGACGGCGTGGTCAGGCTTCAAGGCTGGATGCTTCAATATTCGGATTAAACTTATGGGACAAGCAAAGTTTTCTCATG------GCAT-GCTTCACTTGACGATGAAAATCAAGAAATATCAGTTTGCGTTCACTTTAATTCGAGTATTAAGACTG---GATTTTGCCCCTGGTTTTTAACGTTGGGTGATTATATTGCCATTTTATAAGATCATTCCGGGCTTCAAATGTACTTACGTTTGATCTGGATGAGGATTATACGCTCGAAATATTACCGAGCATATGAAGCAAGCCCAACTGGCAACGCTTCTTCCATTGCTTCAATTGATTAAGGTGAAAAGCAAGGCAGAAATACGTTCAAACAACTGGCCATTTGATCGTTGGGTTGTCCTGAAAGCAAGAGGAAGTTCTTTAGTGGTTTCAATGCTTTCGCGTTGACCCATAGTTGAGTCATGGGTAGTCTAGGACAAGCATACCATGCATGTGGTCGTATAGAAGCATCGTAGGTCTTGATAGCCTGATTACAACTTCTCACACTTTGCGCGATTCAGTCTATCCCATGTGACATGGTATATCTTGATTTGGAGAGCTAGAAGTGTGCCAAGAAGTAGTACCGAAATCTTTCCAGACGGTTGGTGGACGTACTTGTAAACTCTTTGATTATATGCTCGGGATTTTTGATGAAGTCAGGGAGTGCCACGATACTATTGAAAGGTCAGGATAATAATCACCGAGGAAATCACAAACACAGATTGGATTGCTTTCACAAGTCTTAAGATGTTTATTTGGATAGATCCAAGTATACTTTACCTGTTGAGTACTATATCGATTTTCAAAATTTCTGAGCTTGCTGAAACTAAAAGTTATCCTCGATAATACAAAATGCCCTTACTGGATAGTACAACTGACTATGATCATTGCAGTAGTTTTGATTTTGGTTCAAAATACAGTGTTTCAATCAAAGCATGTCTGATATCGAGGGATTAGAGGTCATACTGGTATAATATCGGATCTCTGAGCTTACCGCATTTGTACTTGATTCTCATAAGAATCAGTTTTTGCTTTTAAGAATGATCCATTACAGCTAACACAAGCAACTTGGATCGACTGGTATAGAACTATGGATAAAACTTCCGTGTTTCGCAACATTGTTCATTAACAACTGTTGGAACCCAAACACCGTTTGTTTCTGGCTATGCTGGTTTGAGAAAACGAACCGAGTTTCCCAACAAGTTCCAATAGGTTACAAACCTTGCCCCACGGTCATGCCGGTTAGGAATGGTTTAATACTGGAAGAACAAATATTGTCAAGCTCTAATTGTTGACACTCATACAATTTCCAAGGAGGTCAAGCTCGCAAGATTATTGCTAAAGCGTACTTGAATCATAGACAACGGTGTGCGAAAGATATTGAACAGTAGAAAACTAACCACTGTTTCAATAGCTCTGGATCAGTTCTCAAGAAAAGCCTGAATCGTCGCTCTTCAATTCTGCTGACTCTTGAAAGGTTACATCATTATGAACCTCTAATAATTGTACCAACTGGCAGGATTTGGAAACGATTGAAAAAAAGAGAGAAAGAGTTGTTTGGTCATTAGGGACAATTCCCGTATTCATCTAGTTGGAAATTTTGACTCTTATGAACCAGAACTGTCCCGGATCATATCCGACCAGTGACAAAAAAGCATTAAGAACAAAGAATCAAATCTTTCTTTAGGATTGAGTTATCTTCAAATGATGATCACATTAAGTCAATTTCAGAGTTGCAAAAGTGAAAATAGCATCTGGTGATTTAATTGTAAGGTGCTTTCGATGTAGGTGAAAATGATACGAAAGACTGCCCTACAAGAATTAACGAATATAAACTGCAATGGCAGATTTGTTGATGCTACATTCAGTATGTCATTCTGGATGCAGCGTAGATTTAAGTATTATTGTGAATATTAAAACCTGCCATACAGCCTGTAGCGGAAAAACAGATGCACCTATCTGTAGAGAGTAACGAAAAGACTTTAT---AATGAC----ACTGGCAAACAAACATGGAAGAGCCATTTTCCCCAATATCTCAGGTTTGGGCTAGACTGAATAGAATATCAACGTAAAATAGCTTCTACGTCTAGTGCAAGGGATGGAAACTACTGTGAAAGTAAATTGAGCGTGCAAAGTGTTCCTGTGTCCTTGACAAAACAGAGTGAACGCATTAAAAAGTGCTTT--\n' |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/out.occupancy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.occupancy Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit 12 0 1.0 None Cgla;Kafr;Kbla;Kpha;Kpol;Scas;Scer;Sdai;Skud;Smik;Snag;Suva +12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit 12 0 1.0 None Cgla;Kafr;Kbla;Kpha;Kpol;Scas;Scer;Sdai;Skud;Smik;Snag;Suva +12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit 12 0 1.0 None Cgla;Kafr;Kbla;Kpha;Kpol;Scas;Scer;Sdai;Skud;Smik;Snag;Suva |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/out.partition --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.partition Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +AUTO, 12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit=1-955 +AUTO, 12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit=956-2675 +AUTO, 12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit=2676-6288 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +624 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/simple.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/simple.fa Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,11 @@ +>1 +A-GTAT +>2 +A-G-AT +>3 +A-G-TA +>4 +AGA-TA +>5 +ACa-T- + |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_alignment_0.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_alignment_0.fa Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>1 +ATG-GAGAT +>2 +ATGAGAGAT +>3 +ATGAGACAT +>4 +ATTA-ACAT |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_aln_pk_pi.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_aln_pk_pi.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +mean: 0.7593 +median: 0.7778 +25th percentile: 0.6944 +75th percentile: 0.8611 +minimum: 0.5556 +maximum: 0.8889 +standard deviation: 0.1299 +variance: 0.0169 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_aln_pk_pi_verbose.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_aln_pk_pi_verbose.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,6 @@ +1-2 0.8888888888888888 +1-3 0.7777777777777778 +1-4 0.5555555555555556 +2-3 0.8888888888888888 +2-4 0.6666666666666666 +3-4 0.7777777777777778 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_aln_pk_pis.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_aln_pk_pis.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +1 9 11.1111 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_evo_rate.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_evo_rate.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0.3089 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_tree_simple_pd.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_tree_simple_pd.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +mean: 76.1974 +median: 49.5888 +25th percentile: 40.5054 +75th percentile: 108.1385 +minimum: 24.0 +maximum: 152.8813 +standard deviation: 45.4698 +variance: 2067.502 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_tree_simple_pd_verbose.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_tree_simple_pd_verbose.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,28 @@ +raccoon-bear 26.0 +raccoon-sea_lion 43.4461 +raccoon-seal 43.4521 +raccoon-monkey 147.4653 +raccoon-cat 93.7467 +raccoon-weasel 44.8935 +raccoon-dog 45.5071 +bear-sea_lion 31.047 +bear-seal 31.053 +bear-monkey 135.0661 +bear-cat 81.3475 +bear-weasel 32.4944 +bear-dog 33.108 +sea_lion-seal 24.0 +sea_lion-monkey 143.0726 +sea_lion-cat 89.354 +sea_lion-weasel 40.5009 +sea_lion-dog 48.8621 +seal-monkey 143.0786 +seal-cat 89.36 +seal-weasel 40.5069 +seal-dog 48.8681 +monkey-cat 148.0 +monkey-weasel 140.3308 +monkey-dog 152.8813 +cat-weasel 86.6122 +cat-dog 99.1627 +weasel-dog 50.3095 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_tree_simple_rfd.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_tree_simple_rfd.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +8 0.8 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/test_treeness_over_rcv.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_treeness_over_rcv.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0.35 0.126 0.36 |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple.outgroup.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple.outgroup.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +sea_lion +seal |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple.pruned --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple.pruned Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((sea_lion:11.99700,seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,weasel:18.87953):2.09460):3.87382,dog:25.46154):0.00000; |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple.tre Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154); \ No newline at end of file |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple.tre.pruned --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple.tre.pruned Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((sea_lion:11.99700,seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,weasel:18.87953):2.09460):3.87382,dog:25.46154):0.00000; |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple.tre.rooted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple.tre.rooted Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((((raccoon:19.19959,bear:6.80041):0.84600,dog:25.46154):3.87382,((monkey:100.85930,cat:47.14069):20.59201,weasel:18.87953):2.09460):7.52973,sea_lion:11.99700,seal:12.00300):0.00000; |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple_keep.pruned --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple_keep.pruned Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(raccoon:19.19959,bear:6.80041):0.00000; |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple_other_topology.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple_other_topology.tre Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((sea_lion:19.19959,bear:6.80041):0.84600,((raccoon:11.99700, seal:12.00300):7.52973,((monkey:100.85930,weasel:47.14069):20.59201, cat:18.87953):2.09460):3.87382,dog:25.46154); |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple_prune.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple_prune.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +raccoon +bear |
| b |
| diff -r 000000000000 -r 37b049bf729a test-data/tree_simple_prune_keep.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_simple_prune_keep.txt Mon Mar 28 16:23:18 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +raccoon +bear +sea_lion +seal |