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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e |
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quicktree.xml test-data/example.001.AA.dist.lt.phy test-data/example.001.AA.newick test-data/example.009.AA.dist test-data/example.009.AA.fasta test-data/example.009.AA.newick test-data/example.009.AA.stockholm test-data/example.011.AA.align.newick test-data/example.011.AA.align.params.newick test-data/example.011.AA.clw test-data/example.011.AA.newick test-data/example.011.AA.phy test-data/example_dist_square_phylip.dist test-data/example_dist_square_phylip.newick |
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| diff -r 000000000000 -r 1e89a460d1bd quicktree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quicktree.xml Mon Nov 25 13:13:10 2024 +0000 |
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| b'@@ -0,0 +1,179 @@\n+<tool id="quicktree" name="Quicktree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description></description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.5</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <edam_topics>\n+ <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_0540</edam_operation> <!-- Phylogenetic inference (from molecular sequences) -->\n+ </edam_operations>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">quicktree</requirement>\n+ <requirement type="package" version="3.4">hmmer</requirement> <!-- for file conversion with esl-reformat-->\n+ </requirements>\n+ <version_command>quicktree -v</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+## convert alignment to stockholm before quicktree if needed\n+#if $input_type.format == "align"\n+ esl-reformat -o input.quicktree stockholm \'$input_file\' ##--informat a2m\n+#else\n+ ln -s \'$input_file\' input.quicktree\n+#end if\n+\n+&&\n+\n+quicktree\n+#if $input_type.format =="align"\n+ -in a\n+#else\n+ -in m\n+#end if\n+#if $output_type == \'tree_out\'\n+ -out t\n+#else\n+ -out m\n+#end if\n+$upgma\n+$kimura\n+#if $boot\n+ -boot $boot\n+#end if\n+input.quicktree\n+> \'$output_file\'\n+\n+ ]]></command>\n+ <inputs>\n+ <conditional name="input_type">\n+ <param name="format" type="select" label="Provide an alignment file or a distance matrix?">\n+ <option value="align">Alignment File</option>\n+ <option value="dist">Distance Matrix</option>\n+ </param>\n+ <when value="align">\n+ <param name="input_file" type="data" format="fasta,stockholm,phylip,txt" label="Alignment file" />\n+ </when>\n+ <when value="dist">\n+ <param name="input_file" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist,txt" label="Distance Matrix" help="A distance matrix in phylip format (see help below for details). Can be a square distance matrix or a lower triangle distance matrix." />\n+ </when>\n+ </conditional>\n+ <param argument="-upgma" type="boolean" truevalue="-upgma" falsevalue="" checked="false" label="Use the UPGMA method to construct the tree" help="ignored for distance matrix outputs"/>\n+ <param argument="-kimura" type="boolean" truevalue="-kimura" falsevalue="" checked="false" label="Use the kimura translation for pairwise distances" help="ignored for distance matrix outputs"/>\n+ <param argument="-boot" type="integer" optional="true" min="0" label="Calcuate bootstrap values with n iterations" help="ignored for distance matrix outputs"/>\n+ <param name="output_type" type="select" multiple="false" label="Choose output format">\n+ <option value="dist_out">Distance Matrix (Phylip format)</option>\n+ <option value="tree_out" selected="true">Tree (Newick format)</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="output_file" format="newick" label="${tool.name} on ${on_string}: stockholm format">\n+ <change_format>\n+ <when input="output_type" value="dist_out" format="mothur.dist" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1"><!-- test 1: with fasta input (with reformat) -->\n+ <param name="format" value="align"/>\n+ <param name="input_file" value="example.009.AA.fasta" ftype="fasta"/>\n+ <output name="output_file" file="example.009.AA.newick" ftype="newick"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- test 2: with stockholm input (no reformat)-->\n+ <param name="format" value="align"/>\n+ <param name="input_file" value="example.009.AA.stockholm" ftype="stockholm"/>\n+ <output name="output_fil'..b'k"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- test 4: with phylip distance matrix input (lower triangle distance matrix) -->\n+ <param name="format" value="dist"/>\n+ <param name="input_file" value="example.001.AA.dist.lt.phy" ftype="mothur.dist"/>\n+ <output name="output_file" file="example.001.AA.newick" ftype="newick"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- test 5: with phylip distance matrix input (square distance matrix) -->\n+ <param name="format" value="dist"/>\n+ <param name="input_file" value="example_dist_square_phylip.dist" ftype="mothur.dist"/>\n+ <output name="output_file" file="example_dist_square_phylip.newick" ftype="newick"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- test 6: with phylip alignment input -->\n+ <param name="format" value="align"/>\n+ <param name="input_file" value="example.011.AA.phy" ftype="phylip"/>\n+ <output name="output_file" file="example.011.AA.align.newick" ftype="newick"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- test 7: with distance matrix output -->\n+ <param name="format" value="align"/>\n+ <param name="input_file" value="example.009.AA.fasta" ftype="fasta"/>\n+ <param name="output_type" value="dist_out"/>\n+ <output name="output_file" file="example.009.AA.dist" ftype="mothur.dist"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- test 8: test with all parameters set -->\n+ <param name="format" value="align"/>\n+ <param name="input_file" value="example.011.AA.phy" ftype="phylip"/>\n+ <param name="upgma" value="-upgma"/>\n+ <param name="kimura" value="-kimura"/>\n+ <param name="boot" value="100"/>\n+ <output name="output_file" file="example.011.AA.align.params.newick" ftype="newick"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+QuickTree is an efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies\n+from huge alignments in time less than the age of the universe.\n+\n+\n+**Input**\n+\n+QuickTree accepts both distance matrix and multiple-sequence-aligment inputs. The former should be in PHYLIP format. The latter should be in Stockholm format, which is the native alignment format for the Pfam database.\n+\n+Alignments can be supplied in various other formats (fasta, phylip, clustalw, pfam, psiblast, selex) and will be converted to Stockholm format with the esl-reformat program,\n+which is part of the HMMer package (hmmer.org).\n+\n+**Output**\n+\n+Quicktree will output either a distance matrix (in PHYLIP format, square distance matrix) or a Newick tree.\n+\n+\n+**File Formats**\n+\n+The **distance matrix** input should be in phylip format, it can be a square matrix or a lower triangle matrix.\n+The distance matrix output by quicktree will be a square matrix.\n+\n+Example square distance matrix in phylip format::\n+\n+ 5\n+ Alpha 0.000 1.000 2.000 3.000 3.000\n+ Beta 1.000 0.000 2.000 3.000 3.000\n+ Gamma 2.000 2.000 0.000 3.000 3.000\n+ Delta 3.000 3.000 3.000 0.000 1.000\n+ Epsilon 3.000 3.000 3.000 1.000 0.000\n+\n+Example of a lower triangle matrix::\n+\n+ 7\n+ Mouse\n+ Bovine 1.7043\n+ Lemur 2.0235 1.1901\n+ Orang 2.0593 1.2005 1.5356\n+ Gorilla 1.6664 1.3460 1.4577 1.5935\n+ Chimp 1.7320 1.3757 1.7803 1.7119 1.0635\n+ Human 1.7101 1.3956 1.6661 1.7599 1.0557 0.6933\n+\n+\n+* For more details about the PHYLIP distance matrix format, see https://phylipweb.github.io/phylip/doc/distance.html\n+* For more details about the Newick output format, see https://phylipweb.github.io/phylip/newicktree.html\n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/oxfordjournals.molbev.a040454</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 1e89a460d1bd test-data/example.001.AA.dist.lt.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.001.AA.dist.lt.phy Mon Nov 25 13:13:10 2024 +0000 |
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|
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.001.AA.newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.001.AA.newick Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,283 @@ +( +( +U68661:0.16336, +U68594:0.08766) +:0.03979, +( +( +( +( +( +( +U68681:0.02699, +U68677:0.00387) +:0.05452, +U68669:0.08818) +:0.01678, +( +U68589:0.12797, +U68642:0.13138) +:0.00678) +:0.02517, +U68599:0.15264) +:0.00789, +( +( +( +( +( +U68629:0.04187, +( +( +U68614:0.01334, +U68596:0.02576) +:0.01876, +( +U68607:0.06721, +U68617:0.02437) +:0.00755) +:0.01151) +:0.00357, +( +( +U68601:0.02373, +U68628:0.02152) +:0.01449, +U68634:0.02120) +:0.01546) +:0.05344, +U68616:0.10065) +:0.00718, +( +( +( +U68626:0.04210, +U68623:0.03637) +:0.04538, +U68630:0.08869) +:0.01776, +( +( +( +( +( +( +U68688:0.01010, +U68663:0.01017) +:0.00004, +U68665:0.00000) +:0.00536, +U68679:0.00571) +:0.03386, +( +U68660:0.03763, +U68676:0.01412) +:0.01018) +:0.01469, +U68647:0.04707) +:0.01516, +U68653:0.03330) +:0.04517) +:0.00628) +:0.00866, +U68674:0.10208) +:0.01189) +:0.01188, +( +( +( +( +( +( +( +U68595:0.02056, +U68666:0.02564) +:0.02555, +( +U68636:0.00000, +U68631:0.00602) +:0.02368) +:0.02726, +( +( +( +U68610:0.01866, +U68652:0.01585) +:0.01170, +U68683:0.01609) +:0.00871, +U68671:0.02798) +:0.02742) +:0.02639, +( +U68685:0.05378, +( +U68687:0.04216, +U68592:0.02375) +:0.03065) +:0.04304) +:0.06378, +U68622:0.19663) +:0.02115, +( +( +U68603:0.11984, +U68643:0.19979) +:0.00402, +( +( +( +U68682:0.03023, +U68657:0.03103) +:0.02176, +( +U68627:0.02576, +U68609:0.02869) +:0.04164) +:0.00680, +U68675:0.05209) +:0.04751) +:0.11520) +:0.00569, +( +( +U68608:0.34720, +U68664:0.23588) +:0.01955, +( +U68600:0.05079, +U68591:0.07201) +:0.10552) +:0.01777) +:0.00978) +:0.00173, +( +( +( +( +( +( +( +( +( +( +( +( +U68645:0.02964, +U68619:0.02190) +:0.00546, +U68678:0.01167) +:0.02252, +U68598:0.01558) +:0.00511, +( +U68667:0.01824, +U68673:0.00000) +:0.01816) +:0.00526, +( +( +U68658:0.01841, +U68618:0.00410) +:0.01108, +U68638:0.00140) +:0.02515) +:0.00708, +( +( +( +U68602:0.01531, +U68637:0.01726) +:0.02007, +( +U68613:0.02331, +U68659:0.06238) +:0.01248) +:0.00376, +( +( +U68635:0.01991, +U68686:0.02385) +:0.00384, +U68655:0.07379) +:0.01411) +:0.00346) +:0.01219, +U68624:0.07170) +:0.00617, +( +U68651:0.03189, +U68640:0.04008) +:0.03210) +:0.01574, +( +U68612:0.04507, +U68633:0.01292) +:0.08166) +:0.02775, +( +( +U68648:0.03119, +U68632:0.02264) +:0.01643, +( +U68597:0.02135, +U68605:0.03079) +:0.02728) +:0.06798) +:0.00673, +( +( +( +U68646:0.07691, +U68590:0.05677) +:0.03135, +U68644:0.08129) +:0.02479, +( +( +( +( +U68649:0.03209, +( +U68654:0.03208, +U68639:0.04639) +:0.00768) +:0.00884, +U68606:0.04356) +:0.00811, +U68593:0.05941) +:0.02017, +U68684:0.06550) +:0.00983) +:0.01449) +:0.01477, +( +( +( +( +( +U68680:0.00314, +U68615:0.00000) +:0.04196, +U68670:0.06062) +:0.04225, +U68611:0.08167) +:0.04545, +U68625:0.11382) +:0.00572, +( +( +( +U68668:0.09584, +U68656:0.12526) +:0.01361, +( +U68672:0.02135, +U68621:0.02128) +:0.06214) +:0.01055, +U68662:0.13020) +:0.01409) +:0.00809) +:0.00539); |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.009.AA.dist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.dist Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,10 @@ + 9 + Csa004271 0.00000 0.48921 0.55714 0.47857 0.50000 0.47143 0.50714 0.50000 0.52143 + Xtr21234 0.48921 0.00000 0.33526 0.34682 0.33526 0.31792 0.30636 0.30636 0.31214 + LcaH 0.55714 0.33526 0.00000 0.19209 0.18079 0.32184 0.31250 0.27841 0.28409 + Hsa167996 0.47857 0.34682 0.19209 0.00000 0.06593 0.29143 0.34091 0.31250 0.32955 + Mmu024661 0.50000 0.33526 0.18079 0.06593 0.00000 0.30857 0.35227 0.31818 0.32955 + Dre37936 0.47143 0.31792 0.32184 0.29143 0.30857 0.00000 0.22414 0.17816 0.22989 + LcaM 0.50714 0.30636 0.31250 0.34091 0.35227 0.22414 0.00000 0.09091 0.11932 + Tru14292 0.50000 0.30636 0.27841 0.31250 0.31818 0.17816 0.09091 0.00000 0.11932 + Ola20972 0.52143 0.31214 0.28409 0.32955 0.32955 0.22989 0.11932 0.11932 0.00000 |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.009.AA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.fasta Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,45 @@ +>Csa004271 +---------------------------------MYMAMGHFFDRDDVALKNISEYFKECS +EEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL +HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS +----- +>Xtr21234 +----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQS +KEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL +HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS- +----- +>LcaH +----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQS +HEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL +HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGK +ES--S +>Hsa167996 +MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS +HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL +HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGD +SDNES +>Mmu024661 +MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQS +HEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL +HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGH +GD-ES +>Dre37936 +---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNS +EEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL +HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS +----- +>LcaM +----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENS +DEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL +HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGG +KS--- +>Tru14292 +----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENS +DEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL +HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGS +KS--- +>Ola20972 +----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENS +HEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL +HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGS +KS--- \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.009.AA.newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.newick Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,22 @@ +( +( +Dre37936:0.10177, +( +( +( +Mmu024661:0.03531, +Hsa167996:0.03063) +:0.06297, +LcaH:0.09051) +:0.07497, +( +Xtr21234:0.15038, +Csa004271:0.33883) +:0.01789) +:0.03569) +:0.05109, +Tru14292:0.03661, +( +Ola20972:0.06669, +LcaM:0.05263) +:0.00885); |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.009.AA.stockholm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.stockholm Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,12 @@ +# STOCKHOLM 1.0 + +Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLALHE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS----- +Xtr21234 ----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQSKEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDLHNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS------ +LcaH ----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQSHEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDLHKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGKES--S +Hsa167996 MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES +Mmu024661 MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGHGD-ES +Dre37936 ---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNSEEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDLHKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS----- +LcaM ----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENSDEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDLHKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGGKS--- +Tru14292 ----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENSDEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDLHKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGSKS--- +Ola20972 ----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENSHEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDLHKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS--- +// |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.011.AA.align.newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.011.AA.align.newick Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,244 @@ +( +( +22|Sso-Q97W25:0.30664, +( +20|Sso-Q97V06:0.21441, +19|Sto-Q96ZY0:0.20624) +:0.14658) +:0.03564, +( +( +75|Ath-Q9FXH9:0.21233, +74|Ath-C48C_A:0.24124) +:0.07349, +( +73|Spo-O14325:0.20750, +72|Sce-YL34_Y:0.21424) +:0.08818) +:0.03383, +( +( +( +( +( +( +82|Aga-SANGP0:0.24149, +81|Dme-Q9VUC7:0.27255) +:0.10151, +( +( +( +80|Ath-Q9FNP1:0.32441, +( +79|Fru-SINFRU:0.22655, +78|Hsa-IPI002:0.22858) +:0.08980) +:0.00952, +( +( +77|Cal-CA3667:0.28432, +76|Sce-PEX1_Y:0.29884) +:0.04090, +13|Ncr-NCU081:0.31995) +:0.01510) +:0.00135, +01|Spo-O74941:0.36997) +:0.00411) +:0.02764, +( +( +( +( +( +12|Mmu-IPI001:0.02739, +11|Rno-IPI001:0.02580) +:0.02969, +( +10|Hsa-IPI002:0.00840, +09|Hsa-IPI001:0.00862) +:0.04903) +:0.26665, +( +08|Ncr-NCU083:0.30341, +( +04|Sce-PEX6_Y:0.30322, +03|Cal-CA3485:0.29125) +:0.02682) +:0.02848) +:0.00702, +( +07|Ath-Q9SA70:0.32901, +00|Spo-PEX6_S:0.35281) +:0.01137) +:0.01178, +( +( +06|Aga-SANGP0:0.26226, +05|Dme-AAF587:0.25967) +:0.08570, +02|Cel-O16270:0.37015) +:0.01829) +:0.01621) +:0.02569, +( +14|Mbo-CAD933:0.00000, +( +15|MtU-P96281:0.00000, +16|Mtu-P96281:0.00000) +:0.00000) +:0.00000) +:0.00644, +( +21|Aga-SANGP0:0.34729, +( +18|Dme-Q9VK63:0.28449, +17|Aga-SANGP0:0.28284) +:0.06758) +:0.00867) +:0.01535, +( +( +( +( +( +( +( +( +( +( +( +( +71|Mac-Q8THE2:0.01504, +70|Mma-Q8PXG2:0.01681) +:0.15454, +69|Afu-O28972:0.13421) +:0.02754, +( +68|Mja-YB56_M:0.15837, +( +66|Pho-O59515:0.02351, +65|Pab-Q9V1N2:0.02532) +:0.13887) +:0.00603) +:0.00825, +67|Mth-O27676:0.18666) +:0.01360, +( +56|Tvo-Q97A35:0.01797, +55|Tac-VAT_TH:0.01813) +:0.18933) +:0.00695, +( +( +( +( +64|Sto-Q976H7:0.06577, +63|Sso-Q980U9:0.08116) +:0.07317, +62|Ape-Q9Y910:0.14572) +:0.01843, +61|PaE-Q8ZYN4:0.17174) +:0.01534, +( +( +( +60|Sto-Q975P4:0.10323, +59|Sso-Q97ZZ9:0.11758) +:0.02987, +58|Ape-Q9YC86:0.13255) +:0.02410, +57|PaE-Q8ZTN5:0.16198) +:0.02752) +:0.02156) +:0.00947, +( +54|Mac-Q8TPU1:0.02582, +53|Mma-Q8Q089:0.02726) +:0.21073) +:0.00179, +( +52|Hal-CDCH_H:0.21891, +( +51|Hal-Q9HHW2:0.16094, +50|Hal-Q9HPU1:0.15183) +:0.06466) +:0.01609) +:0.04147, +29|Ana-Q8YUT8:0.28698) +:0.00277, +( +( +( +( +( +( +( +49|Sce-CC48_Y:0.05530, +48|Cal-CA3333:0.05086) +:0.03456, +46|Ncr-NCU000:0.08221) +:0.00567, +47|Spo-CC48_S:0.09093) +:0.04669, +( +( +( +( +( +44|Aga-SANGP0:0.00000, +45|Aga-SANGP0:0.00000) +:0.00000, +43|Dme-Q9V3C3:0.03790) +:0.04874, +( +( +( +41|Mmu-IPI003:0.00210, +( +39|Rno-IPI002:0.00000, +42|Hsa-IPI000:0.00000) +:0.00000) +:0.00061, +40|Mmu-IPI001:0.00151) +:0.01556, +38|Fru-SINFRU:0.01841) +:0.05264) +:0.01404, +( +37|Cel-TER1_C:0.04461, +36|Cel-TER2_C:0.04669) +:0.05204) +:0.02801, +( +( +35|Ath-C48E_A:0.01069, +34|Ath-C48A_A:0.01054) +:0.01288, +33|Ath-C48D_A:0.02533) +:0.09380) +:0.02129) +:0.02630, +31|Pfa-MAL6P1:0.17156) +:0.01277, +32|Gth-Q98S05:0.19589) +:0.03288, +30|Ecu-Q8SSJ5:0.23290) +:0.07549) +:0.01214, +( +28|Spo-O60058:0.27979, +( +27|Sce-AFG2_Y:0.18940, +26|Cal-CA5106:0.18857) +:0.09383) +:0.03449) +:0.00336, +( +25|Ath-C48B_A:0.27738, +( +24|Fru-SINFRU:0.26029, +23|Hsa-IPI000:0.24410) +:0.06114) +:0.01495) +:0.00660) +:0.00134); |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.011.AA.align.params.newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.011.AA.align.params.newick Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,246 @@ +( +( +( +( +( +82|Aga-SANGP0:0.41839, +81|Dme-Q9VUC7:0.41839) +100:0.38250, +( +( +80|Ath-Q9FNP1:0.66857, +( +( +79|Fru-SINFRU:0.34314, +78|Hsa-IPI002:0.34314) +100:0.29594, +13|Ncr-NCU081:0.63908) +43:0.02949) +54:0.08452, +( +77|Cal-CA3667:0.52658, +76|Sce-PEX1_Y:0.52658) +100:0.22650) +61:0.04780) +59:0.04323, +01|Spo-O74941:0.84411) +98:0.13043, +( +( +( +( +( +( +( +( +75|Ath-Q9FXH9:0.34132, +74|Ath-C48C_A:0.34132) +100:0.21621, +( +73|Spo-O14325:0.30561, +72|Sce-YL34_Y:0.30561) +100:0.25192) +99:0.08122, +( +( +( +( +( +( +( +( +( +( +( +( +71|Mac-Q8THE2:0.01629, +70|Mma-Q8PXG2:0.01629) +100:0.24704, +( +( +( +69|Afu-O28972:0.18910, +68|Mja-YB56_M:0.18910) +46:0.01818, +( +66|Pho-O59515:0.02528, +65|Pab-Q9V1N2:0.02528) +100:0.18200) +48:0.03239, +67|Mth-O27676:0.23967) +37:0.02365) +47:0.02629, +( +( +( +( +64|Sto-Q976H7:0.08199, +63|Sso-Q980U9:0.08199) +100:0.10347, +62|Ape-Q9Y910:0.18546) +98:0.03823, +61|PaE-Q8ZYN4:0.22369) +87:0.03740, +( +( +( +60|Sto-Q975P4:0.13104, +59|Sso-Q97ZZ9:0.13104) +99:0.03861, +58|Ape-Q9YC86:0.16966) +96:0.04533, +57|PaE-Q8ZTN5:0.21499) +91:0.04610) +63:0.02853) +26:0.00978, +( +56|Tvo-Q97A35:0.01852, +55|Tac-VAT_TH:0.01852) +100:0.28089) +50:0.03620, +( +52|Hal-CDCH_H:0.32569, +( +51|Hal-Q9HHW2:0.20198, +50|Hal-Q9HPU1:0.20198) +100:0.12371) +27:0.00992) +56:0.01226, +( +54|Mac-Q8TPU1:0.02757, +53|Mma-Q8Q089:0.02757) +100:0.32029) +100:0.10500, +( +( +( +( +( +( +( +49|Sce-CC48_Y:0.05737, +48|Cal-CA3333:0.05737) +100:0.03919, +46|Ncr-NCU000:0.09657) +57:0.00834, +47|Spo-CC48_S:0.10491) +100:0.06175, +( +( +( +( +( +44|Aga-SANGP0:0.00000, +45|Aga-SANGP0:0.00000) +:0.00000, +43|Dme-Q9V3C3:0.03920) +100:0.04707, +( +( +41|Mmu-IPI003:0.00160, +( +40|Mmu-IPI001:0.00106, +( +39|Rno-IPI002:0.00000, +42|Hsa-IPI000:0.00000) +:0.00000) +70:0.00053) +100:0.01655, +38|Fru-SINFRU:0.01814) +100:0.06813) +97:0.02418, +( +37|Cel-TER1_C:0.04879, +36|Cel-TER2_C:0.04879) +100:0.06167) +95:0.02429, +( +( +35|Ath-C48E_A:0.01078, +34|Ath-C48A_A:0.01078) +96:0.01452, +33|Ath-C48D_A:0.02530) +100:0.10945) +97:0.03191) +100:0.05329, +31|Pfa-MAL6P1:0.21995) +72:0.01432, +32|Gth-Q98S05:0.23427) +100:0.06813, +30|Ecu-Q8SSJ5:0.30240) +100:0.15047) +62:0.03749, +29|Ana-Q8YUT8:0.49035) +92:0.04706, +25|Ath-C48B_A:0.53742) +35:0.02074, +( +28|Spo-O60058:0.49172, +( +27|Sce-AFG2_Y:0.26089, +26|Cal-CA5106:0.26089) +100:0.23083) +91:0.06643) +53:0.06655, +( +24|Fru-SINFRU:0.40514, +23|Hsa-IPI000:0.40514) +99:0.21956) +42:0.00366, +22|Sso-Q97W25:0.62836) +54:0.01038) +89:0.13871, +( +18|Dme-Q9VK63:0.49943, +17|Aga-SANGP0:0.49943) +100:0.27802) +23:0.00469, +21|Aga-SANGP0:0.78214) +37:0.01394, +( +14|Mbo-CAD933:0.00000, +( +15|MtU-P96281:0.00000, +16|Mtu-P96281:0.00000) +:0.00000) +:0.00000) +44:0.03029, +( +20|Sso-Q97V06:0.30444, +19|Sto-Q96ZY0:0.30444) +100:0.52193) +96:0.12137, +( +( +( +( +( +( +12|Mmu-IPI001:0.02763, +11|Rno-IPI001:0.02763) +100:0.03428, +( +10|Hsa-IPI002:0.00861, +09|Hsa-IPI001:0.00861) +100:0.05330) +100:0.62798, +07|Ath-Q9SA70:0.68990) +45:0.04898, +( +08|Ncr-NCU083:0.61246, +( +04|Sce-PEX6_Y:0.54705, +03|Cal-CA3485:0.54705) +84:0.06541) +67:0.12642) +67:0.09124, +00|Spo-PEX6_S:0.83012) +68:0.02099, +( +06|Aga-SANGP0:0.42950, +05|Dme-AAF587:0.42950) +100:0.42162) +60:0.09663) +27:0.02680) +44:0.10734, +02|Cel-O16270:1.08188); |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.011.AA.clw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.011.AA.clw Mon Nov 25 13:13:10 2024 +0000 |
| b |
| b'@@ -0,0 +1,852 @@\n+CLUSTAL W (1.83) multiple sequence alignment\n+\n+\n+Spo-PEX6_SCHPO -QLMESFINQNVCQPFVIERKDSFTFLASNEKNISSFKTETDAELVIRPS\n+Spo-O74941 -YAEIELEIEPDWEILLVQVATTFIQFQPLKLIPSSLCLLRTTEVLITPK\n+Cel-O16270 -TCSNIRVMKVSVKINLFGLVKNVAVDNITPNFKFHETISEDAKLSLMRQ\n+Cal-CA3485 -IVDIPLSQIFEYQLKFLTLVDNGNVVNEGDSIRLILTVEYDTNIVLINQ\n+Sce-PEX6_YEAST -LYMETVHSRDLCQIDFTELILEYALPKIGTNSALSDLPCTISRDLLRPA\n+Dme-AAF58736 LIESPVNFVNGRRVN-MTQIKQENFYGNILDRFQIRNCVEHFADEQTIPG\n+Aga-SANGP00000018134 -VANLVKVAKCEPTPKQDVLCQENLVENLNERYTRHRYLQRITEGQHLPA\n+Ath-Q9SA70 -----LLSTKDLFWIFLKCVVKIEIGIQRVAQVVVLDPTLEDASLTQVPV\n+Ncr-NCU08373.1 -LADATTLCEPDLDETVTGTIGPGSVISSYTATTARKAMKPIPPDLLHPK\n+Hsa-IPI00103761.1 -LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPP\n+Hsa-IPI00299182.1 -LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPP\n+Rno-IPI00188277.1 -LLRRPALGWASPGPRRGEPVPGLLGPGTRLAVTELQGLDPESRDHNHPP\n+Mmu-IPI00116764.1 -LLRRPALGWAAPGPRRGEPVPGLLGPGTRLAVTELRGLGQESRDHSHPP\n+Ncr-NCU08118.1 -LAMATVNIEPDWEMLLFQAIPSKANIKVISIDPPLPCIAPDAEIIVAPK\n+Mbo-CAD93306 -AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGS\n+MtU-P96281 -AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGS\n+Mtu-P96281 -AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGS\n+Aga-SANGP00000014403 -----VVGTVRTLWPG-AKVEFNDVSANELNATVTTLDLEDAEEIFLRLE\n+Dme-Q9VK63 -----AMQPLRIVWPEQFKLHCTQLRGKLLKISALHPSLTAAASISLKHV\n+Sto-Q96ZY0 --------------------------------------------MNANTS\n+Sso-Q97V06 --------------------------------------------MATVTS\n+Aga-SANGP00000019182 ----------------------GICGVTQGPSVYG--EVDRHTVIKIDQI\n+Sso-Q97W25 --------------------------------------------------\n+Hsa-IPI00031608.1 -ALGSCCTAWPADGFAAVGASRSRRSLSL-NRLLLVPCLRRVAVWPVLRE\n+Fru-SINFRUP00000053015 -LMGSCCTAWPAEGFSLMSHPPTQLQMDH-SKITPVTCLRCVKTT-VIVG\n+Ath-C48B_ARATH --------------------------------------------------\n+Cal-CA5106 -ILSDSSAGVVSNDITISFPYRQLCGLLLGDRVELVKFPQYASDISISGV\n+Sce-AFG2_YEAST -VLIGEGILVIDEEVTLSTTIRSVGNLILGDRLELKKAPPYATKVTVGSL\n+Spo-O60058 -ALGEAGITQSGIGPLISPLLAKWANLKAFQRVNISQYLKEAEGIKIVAS\n+Ana-Q8YUT8 -----------------------DLFKGFEQLIELVKTLEEKAEIKTD--\n+Ecu-Q8SSJ5 -TLKKALIFSTSVPPAIVRDGRFNLRIRITDTVKLYRVIPVVSKLNFLPI\n+Pfa-MAL6P1.232 -RMKRHTICIIDLDERINKVARKNLRVCLGDVVYVKSCIPYGKKIQVLPI\n+Gth-Q98S05 -KIKKKTVCIINCELRINKTVRENLNIGIGDIVTIHHFLKFGKRIHVLPF\n+Ath-C48D_ARATH -TMKRKTVCIATCDERMNKVVRSNLRVRLGDVISVHQCVKYGNRVHILPL\n+Ath-C48A_ARATH -TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPV\n+Ath-C48E_ARATH -TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPV\n+Cel-TER2_CAEEL -KMKRRTVSIVNCPNKMNKVVRNNLRSRLGDVVSISSALEYGKRVHVLPI\n+Cel-TER1_CAEEL -KMKRKSVAIISCPNRMNRVVRNNLRIRLGDVVSITPALSYGTRIHVLPI\n+Fru-SINFRUP00000067653 -KMKRRTVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Rno-IPI00212014.1 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Mmu-IPI00122342.3 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Mmu-IPI00318619.1 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Hsa-IPI00022774.1 -KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPI\n+Dme-Q9V3C3 -KMRRKTVCIVTCPDRMNRVVRNNLCVHLSDVVSVQSCVKYGKRVRILPI\n+Aga-SANGP00000022801 -KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPI\n+Aga-SANGP00000021747 -KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPI\n+Ncr-NCU00018.1 -TMKRKTVLIVDLDDRLNRVVRHNLRVKHGDIITIHPCIKYAKRIAVLPI\n+Spo-CC48_SCHPO -TMRRKTVLIVEMEDRINRVVRNNLRVRLGDIVTINPCIKYAERISVLPL\n+Cal-CA3333 -TMKRKTVLIVDMPDRVNRCVRNNLRVRLGDIVTVHPCIKYANRISVLPI\n+Sce-CC48_Y'..b'FNDFIKILANVKPSVNKETLKMYEEFIQRI\n+Sso-Q97V06 VKLEDFMDVLKRVKASLDRQTLIMYEKFFERR\n+Aga-SANGP00000019182 VTMAHLRSALQDVRPSLTKEQIDWYHSYANRL\n+Sso-Q97W25 LTREDLIDALNKIHPSVKKRLSKGSSSNDHET\n+Hsa-IPI00031608.1 VKQEHFLKSLKTVKPSLSCKDLALYENLFKKE\n+Fru-SINFRUP00000053015 LKHRYFVQALSRMRPSLTEQQINSYQ------\n+Ath-C48B_ARATH VFNRHFQTAKSSLKPALTIEEVETYSSFRKAA\n+Cal-CA5106 VTNKHFEHALKGISRGITPEMLEYYEKFSKKS\n+Sce-AFG2_YEAST VELRHFEKAFKGIARGITPEMLSYYEEFALRS\n+Spo-O60058 ICQAHFKTALLALRKAITRDMLEYYASFSESV\n+Ana-Q8YUT8 ITTDDFNYAYKVLTEQRPD-------------\n+Ecu-Q8SSJ5 LRPDHLVQSLKTARRSVSEKEVERYEAFARSM\n+Pfa-MAL6P1.232 ITRHHFKEGLAGARRSVSQADLIKYDNFRIKF\n+Gth-Q98S05 ITKEHFLEAMKYARRSVSDSDIRKYEMFAQKL\n+Ath-C48D_ARATH IKAGHFEESMKYARRSVSDADIRKYQAFAQTL\n+Ath-C48A_ARATH IKAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+Ath-C48E_ARATH IRAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+Cel-TER2_CAEEL ITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+Cel-TER1_CAEEL ITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+Fru-SINFRUP00000067653 IRKDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Rno-IPI00212014.1 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Mmu-IPI00122342.3 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Mmu-IPI00318619.1 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Hsa-IPI00022774.1 IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+Dme-Q9V3C3 ITSAHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+Aga-SANGP00000022801 ITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+Aga-SANGP00000021747 ITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+Ncr-NCU00018.1 LTKRHFEEAMSMARRSVSDVEIRRYEAFSQQM\n+Spo-CC48_SCHPO VQRHHVEEAMKMARRSVSDAEVRRYEAYAHQL\n+Cal-CA3333 ITRAHFEEAMKTAKRSVSDAELRRYESYAQQL\n+Sce-CC48_YEAST ITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM\n+Hal-Q9HPU1 VTMAHFEAALGEVTASVDADVKENYEEIEQRF\n+Hal-Q9HHW2 LSIEHFEQALEEVDSNAGSETQAFEKPAEAV-\n+Hal-CDCH_HALN1 VGMAHFRAAMENVRPTITDDLMEYYDQVEDQF\n+Mma-Q8Q089 VRQKHFLQAIEETGPSVTPDTMKYYQAIRGEL\n+Mac-Q8TPU1 VRQKHFLQAIEETGPSVTPDTMKYYEAIKGEL\n+Tac-VAT_THEAC VSQKNFLDALKTIRPSVDEEVIKFYRTLSETM\n+Tvo-Q97A35 VSQKNFIDALKTIRPSIDEEVIKFYKSISETM\n+PaE-Q8ZTN5 VSMKHFEEALKRIPPSLTPEDIRRYEEIAKRL\n+Ape-Q9YC86 VEMRHFLEALKKVPPSLTKEDILRYERLAKEL\n+Sso-Q97ZZ9 ITMQDFLDTMKIVTPSLTKADIMRYENMVKEI\n+Sto-Q975P4 VTKEDFNKALEVVKPSLTAADIQRYERLAKEL\n+PaE-Q8ZYN4 VSMRHFEEAMKKVRPSITPDMLKFYESWLEKA\n+Ape-Q9Y910 VSMRHFEVALKKVKPSVTPQMVEYYKRWLETV\n+Sso-Q980U9 VSLRHFEEAMRKVKPSVTQDMLQFYQNWVEKA\n+Sto-Q976H7 VEKRHFDIALKKVRPSVTMDMIQFYQNWLEKA\n+Pab-Q9V1N2 VTMKDFEEALRKIGPSVSKETMEYYRKIQEQF\n+Pho-O59515 VTMKDFEEALKKIGPSVSKETMEYYRKIQEQF\n+Mth-O27676 VSMKYFLEAMEKVKPKGGVEEQVQYH------\n+Mja-YB56_METJA IKKEHFMKALEKIKPSVSKEDMRVYEKLAQEY\n+Afu-O28972 ITKKHFEEALKKVRPSLTKEDVEKYEKLIEDF\n+Mma-Q8PXG2 LSKRHFEKAIRRVKPTTSRETLSAYEKSAELF\n+Mac-Q8THE2 LSKRHFERAIRRVRPTTSRETLSAYEKSAELF\n+Sce-YL34_YEAST VTMSDFRSALRKIKPSVSDKDRLKYDRLNKKM\n+Spo-O14325 VTNADFELAFKNIKPSVSDRDRQKYQRLAKRW\n+Ath-C48C_ARATH IKTRHFEQALSLVSPSVNKQQRRHYDALSTKL\n+Ath-Q9FXH9 TKMVHFEEASSRMQSGR---------------\n+Sce-PEX1_YEAST VTINDLLEACQETKPSISTSELVKLRGIYDRF\n+Cal-CA3667 ITHENFLESLKETKPSISHSEKIKLTKIYKEF\n+Hsa-IPI00296368.2 ISQSHLMTALGHTRPSISEDDWKNFAELYESF\n+Fru-SINFRUP00000064701 LSAAHLNAALAVTRPSLSRDDWNRYTNLYEAF\n+Ath-Q9FNP1 ITDPLLKSIASKTKPSVSETEKQKLYDIYSQF\n+Dme-Q9VUC7 LKQKHLIESFQTTRPSLSASDVAKYHRTYARF\n+Aga-SANGP00000012419 VSQRHLAEAFSSTRPSLSPRDIAKYRETYARF\n+ . \n' |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.011.AA.newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.011.AA.newick Mon Nov 25 13:13:10 2024 +0000 |
| b |
| @@ -0,0 +1,244 @@ +( +( +Ath-C48B_ARATH:0.27687, +( +Fru-SINFRUP00000053015:0.25657, +Hsa-IPI00031608.1:0.23904) +:0.05950) +:0.01896, +( +( +( +( +( +( +( +( +( +( +( +Mac-Q8THE2:0.01503, +Mma-Q8PXG2:0.01681) +:0.15462, +Afu-O28972:0.13413) +:0.02758, +( +Mja-YB56_METJA:0.15861, +( +Pho-O59515:0.02344, +Pab-Q9V1N2:0.02540) +:0.13863) +:0.00599) +:0.00858, +Mth-O27676:0.18633) +:0.01469, +( +Tvo-Q97A35:0.01810, +Tac-VAT_THEAC:0.01800) +:0.18824) +:0.00665, +( +( +( +( +Sto-Q976H7:0.06580, +Sso-Q980U9:0.08113) +:0.07346, +Ape-Q9Y910:0.14543) +:0.01888, +PaE-Q8ZYN4:0.17128) +:0.01558, +( +( +( +Sto-Q975P4:0.10330, +Sso-Q97ZZ9:0.11751) +:0.02960, +Ape-Q9YC86:0.13282) +:0.02293, +PaE-Q8ZTN5:0.16102) +:0.02888) +:0.02144) +:0.00913, +( +Mac-Q8TPU1:0.02580, +Mma-Q8Q089:0.02728) +:0.21088) +:0.00177, +( +Hal-CDCH_HALN1:0.21715, +( +Hal-Q9HHW2:0.16180, +Hal-Q9HPU1:0.15096) +:0.06537) +:0.01670) +:0.04196, +Ana-Q8YUT8:0.28915) +:0.00398, +( +( +( +( +( +( +( +Sce-CC48_YEAST:0.05504, +Cal-CA3333:0.05111) +:0.03444, +Ncr-NCU00018.1:0.08233) +:0.00576, +Spo-CC48_SCHPO:0.09084) +:0.04654, +( +( +( +( +( +Aga-SANGP00000022801:0.00000, +Aga-SANGP00000021747:0.00000) +:0.00000, +Dme-Q9V3C3:0.03778) +:0.04856, +( +( +( +Mmu-IPI00318619.1:0.00210, +( +Rno-IPI00212014.1:0.00000, +Hsa-IPI00022774.1:0.00000) +:0.00000) +:0.00061, +Mmu-IPI00122342.3:0.00151) +:0.01555, +Fru-SINFRUP00000067653:0.01842) +:0.05282) +:0.01395, +( +Cel-TER1_CAEEL:0.04461, +Cel-TER2_CAEEL:0.04668) +:0.05213) +:0.02771, +( +( +Ath-C48E_ARATH:0.01070, +Ath-C48A_ARATH:0.01054) +:0.01287, +Ath-C48D_ARATH:0.02534) +:0.09410) +:0.02143) +:0.02599, +Pfa-MAL6P1.232:0.17187) +:0.01311, +Gth-Q98S05:0.19555) +:0.03221, +Ecu-Q8SSJ5:0.23357) +:0.07766) +:0.01483, +( +Spo-O60058:0.27814, +( +Sce-AFG2_YEAST:0.17646, +Cal-CA5106:0.17212) +:0.10076) +:0.03820) +:0.00306, +( +( +( +( +( +( +Aga-SANGP00000012419:0.24004, +Dme-Q9VUC7:0.27107) +:0.09885, +( +( +( +Ath-Q9FNP1:0.32294, +( +Fru-SINFRUP00000064701:0.22651, +Hsa-IPI00296368.2:0.22862) +:0.08699) +:0.01380, +( +( +Cal-CA3667:0.28476, +Sce-PEX1_YEAST:0.30056) +:0.03999, +Ncr-NCU08118.1:0.32086) +:0.01510) +:0.00261, +Spo-O74941:0.37022) +:0.00623) +:0.02873, +( +( +( +( +( +Mmu-IPI00116764.1:0.02738, +Rno-IPI00188277.1:0.02581) +:0.03039, +( +Hsa-IPI00299182.1:0.00853, +Hsa-IPI00103761.1:0.00849) +:0.04833) +:0.26630, +( +Ncr-NCU08373.1:0.30583, +( +Sce-PEX6_YEAST:0.29683, +Cal-CA3485:0.28437) +:0.02913) +:0.03099) +:0.00828, +( +Ath-Q9SA70:0.33122, +Spo-PEX6_SCHPO:0.35357) +:0.01003) +:0.01174, +( +( +Aga-SANGP00000018134:0.25801, +Dme-AAF58736:0.25408) +:0.09657, +Cel-O16270:0.37783) +:0.01559) +:0.01762) +:0.02162, +( +Aga-SANGP00000019182:0.36243, +( +Mbo-CAD93306:0.00000, +( +MtU-P96281:0.00000, +Mtu-P96281:0.00000) +:0.00000) +:0.00000) +:0.02443) +:0.01178, +( +Dme-Q9VK63:0.27762, +Aga-SANGP00000014403:0.27426) +:0.08853) +:0.01226, +( +( +( +Ath-Q9FXH9:0.21646, +Ath-C48C_ARATH:0.24833) +:0.06504, +( +Spo-O14325:0.20405, +Sce-YL34_YEAST:0.21117) +:0.09282) +:0.03673, +( +Sso-Q97W25:0.31405, +( +Sso-Q97V06:0.21384, +Sto-Q96ZY0:0.20325) +:0.14231) +:0.03661) +:0.00356) +:0.00724); |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example.011.AA.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.011.AA.phy Mon Nov 25 13:13:10 2024 +0000 |
| b |
| b'@@ -0,0 +1,674 @@\n+ 83 471\n+Spo-PEX6_S QLMESFINQNVCQPFVIERKDSFTFLASNEKNISSFKTETDAELVIRPSFDENESVISEE\n+Spo-O74941 YAEIELEIEPDWEILLVQVATTFIQFQPLKLIPSSLCLLRTTEVLITPKDSVADSLCVFL\n+Cel-O16270 TCSNIRVMKVSVKINLFGLVKNVAVDNITPNFKFHETISEDAKLSLMRQNIREKHHLKQI\n+Cal-CA3485 IVDIPLSQIFEYQLKFLTLVDNGNVVNEGDSIRLILTVEYDTNIVLINQSELVFINNADF\n+Sce-PEX6_Y LYMETVHSRDLCQIDFTELILEYALPKIGTNSALSDLPCTISRDLLRPAVKLVLLLPNGF\n+Dme-AAF587 LIESPVNFVNGRRVNMTQIKQENFYGNILDRFQIRNCVEHFADEQTIPGPAETEVILSNY\n+Aga-SANGP0 VANLVKVAKCEPTPKQDVLCQENLVENLNERYTRHRYLQRITEGQHLPASSDVDFILGRY\n+Ath-Q9SA70 LLSTKDLFWI----FLKCVVKIEIGIQRVAQVVVLDPTLEDASLTQVPVMLVPTYMGQQL\n+Ncr-NCU083 LADATTLCEPDLDETVTGTIGPGSVISSYTATTARKAMKPIPPDLLHPKDVQAVMLKHYF\n+Hsa-IPI001 LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPPLGGGDSLGRYL\n+Hsa-IPI002 LLRRPALGWASLGPRRGEPVPGLLGPGTRLAVTELRGLCPESGDSSRPPDPLMGEIQRYL\n+Rno-IPI001 LLRRPALGWASPGPRRGEPVPGLLGPGTRLAVTELQGLDPESRDHNHPPDPLVGEIQRYL\n+Mmu-IPI001 LLRRPALGWAAPGPRRGEPVPGLLGPGTRLAVTELRGLGQESRDHSHPPDPLVGEIQRYL\n+Ncr-NCU081 LAMATVNIEPDWEMLLFQAIPSKANIKVISIDPPLPCIAPDAEIIVAPKRGIRKHLQEWF\n+Mbo-CAD933 AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGSQSVPVTLRQAL\n+MtU-P96281 AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGSQSVPVTLRQAL\n+Mtu-P96281 AISRTAAVAGDTAVLLDDVTLSNAGLREGTEVIVSPVVYGARSVTLSGSQSVPVTLRQAL\n+Aga-SANGP0 VVGTVRTLWPGAKVEFND---VSANELNATVTTLD--LEDAEEIFLRLEKNGFLLLKYQL\n+Dme-Q9VK63 AMQPLRIVWP-EQFKLHC---TQLRGKLLKISALHPSLTAAASISLKHVVQLDAILKRDM\n+Sto-Q96ZY0 ---------------MNANTSTSPTSSL---LSTYINLGIIILTFVIPL--IFIYFMRMM\n+Sso-Q97V06 ---------------MATVTSNNSTIGLGLSSNTLQLVILTILFFLVPL--IWIYFSRRM\n+Aga-SANGP0 -----GICGVTQGPSVYGEVDRHTVIKI-DQILYHPA-----------------------\n+Sso-Q97W25 VL------------LMKIFGKSTAKFAYSDK-----------------------------\n+Hsa-IPI000 ALGSCCTAWPADGFAAVGASRSRRSLSL-NRLLLVPCLRRVAVWPVLRETAALEAAQELL\n+Fru-SINFRU LMGSCCTAWPAEGFSLMSHPPTQLQMDH-SKITPVTCLRCVKT-TVIVGSRLHELVKDML\n+Ath-C48B_A MLETESVCDNKWRA---------------------EA-----------------------\n+Cal-CA5106 ILSDSSAGVVSNDITISFPYRQLCGLLLGDRVELVKFPQYASDISISGVEDVSALIGLVY\n+Sce-AFG2_Y VLIGEGILVIDEEVTLSTTIRSVGNLILGDRLELKKAPPYATKVTVGSLLECEEKVIQKL\n+Spo-O60058 ALGEAGITQSGIGPLISPLLAKWANLKAFQRVNISQYLKEAEGIKIVASEPIESLIRKEL\n+Ana-Q8YUT8 ----------D---LFKG---FEQLIELVKTLEEKAEIKTDFQINSRSM-----------\n+Ecu-Q8SSJ5 TLKKALIFSTSVPPAIVRDGRFNLRIRITDTVKLYRVIPVVSKLNFLPIGNIDEFVRPFL\n+Pfa-MAL6P1 RMKRHTICIIDLDERINKVARKNLRVCLGDVVYVKSCIPYGKKIQVLPIDTLEIFLKPYF\n+Gth-Q98S05 KIKKKTVCIINCELRINKTVRENLNIGIGDIVTIHHFLKFGKRIHVLPFGNIEDFLKPYF\n+Ath-C48D_A TMKRKTVCIATCDERMNKVVRSNLRVRLGDVISVHQCVKYGNRVHILPLGNIDAYLKPYF\n+Ath-C48A_A TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPVGNLDAYLKPYF\n+Ath-C48E_A TMKRKTVCIATCEERMNKVVRSNLRVRLGDVISVHQCVKYGKRVHILPVGNLDAYLKPYF\n+Cel-TER2_C KMKRRTVSIVNCPNKMNKVVRNNLRSRLGDVVSISSALEYGKRVHVLPIGNLDVFLRPYF\n+Cel-TER1_C KMKRKSVAIISCPNRMNRVVRNNLRIRLGDVVSITPALSYGTRIHVLPIGNLDVFLKPYF\n+Fru-SINFRU KMKRRTVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Rno-IPI002 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Mmu-IPI001 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Mmu-IPI003 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Hsa-IPI000 KMKRRAVCIVTCSDRMNRVVRNNLRVRLGDVISIQPCVKYGKRIHVLPIGNLEVYLKPYF\n+Dme-Q9V3C3 KMRRKTVCIVTCPDRMNRVVRNNLCVHLSDVVSVQSCVKYGKRVRILPIGNLEIYLKPYF\n+Aga-SANGP0 KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPIGNLDVYLKPYF\n+Aga-SANGP0 KMRRKTVCIVNCPDRMNRVVRNNLRVWLGDVVMIQSCVKYGKRVHILPIGNLDVYLKPYF\n+Ncr-NCU000 TMKRKTVLIVDLDDRLNRVVRHNLRVKHGDIITIHPCIKYAKRIAVLPIGSLDVFLAPYF\n+Spo-CC48_S TMRRKTVLIVEMEDRINRVVRNNLRVRLGDIVTINPCIKYAERISVLPLGSLDVYLKPYF\n+Cal-CA3333 TMKRKTVLIVDMPDRVNRCVRNNLRVRLGDIVTVHPCIKYANRISVLPIGSLDLYLKPYF\n+Sce-CC48_Y TMKRKTVLIVELEDRINRVVRNNLRIRLGDLVTIHPCIKYATRISVLPIGNLDVFLKPYF\n+Hal-Q9HPU1 SMGRAARVWPDDGDRIDGRLRKEADVGIDDQVTVEPAIKPAGGVTVALPRGNAPMVRDRL\n+Hal-Q9HHW2 ALGRTARVWPDAGRRIDGQLRQAANVSIDDRVEVEKTVEPADRVTVSLPRGDGSHLREHL\n+Hal-CDCH_H TLETTAKVWRDWNTRIDGFTRQNAEVGIGERVKIRKAAEKADTLVLAPPGSDAGMVKR'..b'SPSLSITELKKYEMLRDQF\n+LPFTYTGADFYALEDISVMVTEQDFLDAHRELVPSVSAGELEHYEQVRAMF\n+CPPQLTGADLYSLGSSALMLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+CPPQLTGADLYSLGSSALMLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+CPPQLTGADLYSLRSSALLLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+CPPQLTGADLYSLRSSALLLTMEDLLQAAARLQPSVSEQELLRYKRIQRKF\n+RTDGFTGADLQALAGPQVVVNWKHLYKALDATRASISVKERKRLERIYHEF\n+GLDGYSAADCVALSIDAANVTAADLATARETVRASLDPLQVASLRKFTKGD\n+GLDGYSAADCVALSIDAANVTAADLATARETVRASLDPLQVASLRKFTKGD\n+GLDGYSAADCVALSIDAANVTAADLATARETVRASLDPLQVASLRKFTKGD\n+RTAGCSGSEIEAISFDVETIEWEHFEHALGVVRPRTSPELLRLYEEYLKQH\n+LTEGYSGAEIQAVSFEAEDVKWTDFEHALKAVPPRTSPELLKLYEDYLKRK\n+ITDGYTPADLKLVGVARTTLTFNDFIKILANVKPSVNKETLKMYEEFIQRI\n+LTENYTPADLKLVGNLRTEVKLEDFMDVLKRVKASLDRQTLIMYEKFFERR\n+QTERYSGADLQNLDLNATVVTMAHLRSALQDVRPSLTKEQIDWYHSYANRL\n+QTEGYSGADLAALGESNRTLTREDLIDALNKIHPSVKKRLSKGSSSNDHET\n+ETCFFSGADLRNLGLDATTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKE\n+KTELYSGADLQNLNLEASALKHRYFVQALSRMRPSLTEQQINSYQ------\n+ETDLFTGAELEGLNIAATAVFNRHFQTAKSSLKPALTIEEVETYSSFRKAA\n+LTDGCSGAEVTLLNKEATTVTNKHFEHALKGISRGITPEMLEYYEKFSKKS\n+RTEGYSGAEVVLLDLDVAKVELRHFEKAFKGIARGITPEMLSYYEEFALRS\n+KTEGCSGAEVVALDLEAKEICQAHFKTALLALRKAITRDMLEYYASFSESV\n+MTQDWNGADLTLLDPSEIKITTDDFNYAYKVLTEQRPD-------------\n+ATDKFSGADLSEIEDPVPYLRPDHLVQSLKTARRSVSEKEVERYEAFARSM\n+KTAGFSGADLAELDDDNIEITRHHFKEGLAGARRSVSQADLIKYDNFRIKF\n+ATSGFSGADITEIIDPVPEITKEHFLEAMKYARRSVSDSDIRKYEMFAQKL\n+YTQGFSGADITEIDEEEIEIKAGHFEESMKYARRSVSDADIRKYQAFAQTL\n+YTQGFSGADITEIVDEVSEIKAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+YTQGFSGADITEIDDEVSEIRAAHFEESMKYARRSVSDADIRKYQAFAQTL\n+NTVGFSGADLTEIADPVPEITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+NTVGFSGADLTEIVDPVPEITRAHFEEAMKFARRSVTDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRKDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSVADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+MTNGFSGADLTEIDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL\n+VTQGFSGADLTEIDDPVPEITSAHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+VTQGFSGADLTEIEDPVPEITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+VTQGFSGADLTEIEDPVPEITRDHFEEAMKFARRSVSDNDIRKYEMFAQTL\n+KTHGFSGADLGFIEDPVPELTKRHFEEAMSMARRSVSDVEIRRYEAFSQQM\n+ATHGFSGADLEFVDEDASQVQRHHVEEAMKMARRSVSDAEVRRYEAYAHQL\n+ITHGFSGADLSYIEDPVPYITRAHFEEAMKTAKRSVSDAELRRYESYAQQL\n+ATQGFSGADLLYIVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM\n+RMDGFVGADVEALSVGNVRVTMAHFEAALGEVTASVDADVKENYEEIEQRF\n+RTDGYVGADIEAVNVDEIELSIEHFEQALEEVDSN-AGSETQAFEKPAEAV\n+RADGYVGSDLANIDEDADDVGMAHFRAAMENVRPTITDDLMEYYDQVEDQF\n+LTDQYTGADIAAVDLHAKSVRQKHFLQAIEETGPSVTPDTMKYYQAIRGEL\n+FTDQYTGADIAAVDLHAKKVRQKHFLQAIEETGPSVTPDTMKYYEAIKGEL\n+RTEGYVGADLENLNPDATSVSQKNFLDALKTIRPSVDEEVIKFYRTLSETM\n+RTEGYVGADLENLNPDATQVSQKNFIDALKTIRPSIDEEVIKFYKSISETM\n+RTEGYTGADIAALTVKAKPVSMKHFEEALKRIPPSLTPEDIRRYEEIAKRL\n+MTEGYTGADIEAVKLEVGKVEMRHFLEALKKVPPSLTKEDILRYERLAKEL\n+KLEGYTGADIEALSNLEIKITMQDFLDTMKIVTPSLTKADIMRYENMVKEI\n+KTEGYTGADIEALNNAKVIVTKEDFNKALEVVKPSLTAADIQRYERLAKEL\n+RTEGYSGADLELLDINAKEVSMRHFEEAMKKVRPSITPDMLKFYESWLEKA\n+RTEGYTGADIEALDINAAEVSMRHFEVALKKVKPSVTPQMVEYYKRWLETV\n+KTEGYTGADLAALKVNGVKVSLRHFEEAMRKVKPSVTQDMLQFYQNWVEKA\n+KTEGYTGADLAALKGKGVLVEKRHFDIALKKVRPSVTMDMIQFYQNWLEKA\n+RTEGYTGADIAAVIRRLAKVTMKDFEEALRKIGPSVSKETMEYYRKIQEQF\n+RTEGYTGADIAAVIKQKAKVTMKDFEEALKKIGPSVSKETMEYYRKIQEQF\n+KTEGYVGADIEAVNMDAEEVSMKYFLEAMEKVKPKGGVEEQVQYH------\n+KTEGYTGADIEALRLKVSKIKKEHFMKALEKIKPSVSKEDMRVYEKLAQEY\n+KTEGYSGADIEAVAAKKLKITKKHFEEALKKVRPSLTKEDVEKYEKLIEDF\n+MTEGYVGADIEGIKAAEVRLSKRHFEKAIRRVKPTTSRETLSAYEKSAELF\n+MTEGYVGADIEGIKAGDVRLSKRHFERAIRRVRPTTSRETLSAYEKSAELF\n+KCNNFSGADLAALSGEEIIVTMSDFRSALRKIKPSVSDKDRLKYDRLNKKM\n+RCSNFSGADLAALALEPIRVTNADFELAFKNIKPSVSDRDRQKYQRLAKRW\n+NCEGFSGADLAHLDITQCTIKTRHFEQALSLVSPSVNKQQRRHYDALSTKL\n+RCENFSGADLEALGSYPRRTKMVHFEEASSRMQSGR---------------\n+KTAGFSGADLQGLSTSAAVVTINDLLEACQETKPSISTSELVKLRGIYDRF\n+KTTGFSGADMQGLNKSKVLITHENFLESLKETKPSISHSEKIKLTKIYKEF\n+VTDSFTGADLKALNQPGPAISQSHLMTALGHTRPSISEDDWKNFAELYESF\n+ATEQFTGADLKALLRPGLLLSAAHLNAALAVTRPSLSRDDWNRYTNLYEAF\n+MTEGFSGADLQALTGTTPIITDPLLKSIASKTKPSVSETEKQKLYDIYSQF\n+KTANYTGADIQSILAKKISLKQKHLIESFQTTRPSLSASDVAKYHRTYARF\n+KSEYYTGADIRSIVPEQITVSQRHLAEAFSSTRPSLSPRDIAKYRETYARF\n+\n+\n' |
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example_dist_square_phylip.dist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_dist_square_phylip.dist Mon Nov 25 13:13:10 2024 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 1e89a460d1bd test-data/example_dist_square_phylip.newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_dist_square_phylip.newick Mon Nov 25 13:13:10 2024 +0000 |
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