| Previous changeset 24:098451b762fb (2021-04-20) Next changeset 26:6d89dc242c2a (2021-06-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9" |
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modified:
hyphy_relax.xml macros.xml test-data/busted-out1.json test-data/gard-out1.json test-data/gard-out1.nex test-data/relax-out1.json |
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added:
test-data/busted-in2.nex test-data/busted-out2-1.json test-data/busted-out2-2.json test-data/relax-in2.nex test-data/relax-out2-1.json test-data/relax-out2-2.json |
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| diff -r 098451b762fb -r a4c5dc437558 hyphy_relax.xml --- a/hyphy_relax.xml Tue Apr 20 19:55:48 2021 +0000 +++ b/hyphy_relax.xml Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| @@ -1,11 +1,9 @@ <?xml version="1.0"?> -<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" profile="19.09"> +<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy1" profile="19.09"> <description>Detect relaxed selection in a codon-based phylogenetic framework</description> <macros> <import>macros.xml</import> - <token name="@OPERATION@">RELAX</token> - <token name="@operation@">relax</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @@ -13,42 +11,56 @@ export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" && hyphy relax --alignment ./$input_file - #if $input_nhx: - --tree ./input.nhx - #end if - --models '$analysisType' + @INPUT_TREE@ + --models '$models' --code '$gencodeid' - #if $treeAnnotations == "2": - --test TEST - --reference REFERENCE - #else: - --test TEST + --test '$test' + #if $reference: + --reference '$reference' #end if - > '$relax_log' ; - @CATCH_ERROR@ + @advanced_options@ + --output '$relax_output' + @ERRORS@ ]]></command> <inputs> <expand macro="inputs"/> <expand macro="gencode"/> - <param argument="--model" name="analysisType" type="select" label="Analysis Type" > + <param argument="--models" type="select" label="Analysis Type" > <option value="All">All</option> <option value="Minimal">Minimal</option> </param> - <param name="treeAnnotations" type="select" label="Tree Annotations" help = "Is there one or two sets of annotated branches in the Newick file?"> - <option value="1">TEST only</option> - <option value="2">TEST and REFERENCE</option> + <param argument="--test" type="text" value="Unlabeled branches" optional="false" label="Branches to use as the test set"> + <sanitizer invalid_char=""> + <valid initial="default" /> + </sanitizer> </param> + <param argument="--reference" type="text" optional="true" label="Branches to use as the reference set"> + <sanitizer invalid_char=""> + <valid initial="default" /> + </sanitizer> + </param> + <expand macro="srv" /> </inputs> <outputs> - <data name="relax_log" format="txt"/> <data name="relax_output" format="hyphy_results.json"/> + <expand macro="alternative_model_output" /> </outputs> <tests> <test> <param name="input_file" ftype="fasta" value="relax-in1.fa"/> <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/> + <param name="test" value="TEST" /> <output name="relax_output" file="relax-out1.json" compare="sim_size"/> </test> + <test> + <param name="input_file" ftype="nex" value="relax-in2.nex"/> + <param name="srv_options" value="specify" /> + <param name="save_alternative_model" value="true" /> + <param name="test" value="PR" /> + <param name="srv" value="Yes" /> + <output name="relax_output" file="relax-out2-1.json" compare="sim_size"/> + <output name="alternative_model" file="relax-out2-2.json" compare="sim_size"/> + </test> </tests> <help><![CDATA[ RELAX: a test for selection differences |
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| diff -r 098451b762fb -r a4c5dc437558 macros.xml --- a/macros.xml Tue Apr 20 19:55:48 2021 +0000 +++ b/macros.xml Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| @@ -93,13 +93,45 @@ </param> </xml> + <xml name="srv"> + <conditional name="advanced" label="Advanced options"> + <param name="srv_options" type="select" label="Set advanced parameters" help="If these parameters are not set, RELAX will calculate appropriate values at runtime"> + <option value="defaults">Calculate</option> + <option value="specify">Specify values</option> + </param> + <when value="defaults" /> + <when value="specify"> + <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" /> + <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" /> + <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Alpha rate classes to include in the model" /> + <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" /> + <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" /> + <param name="save_alternative_model" type="boolean" label="Save alternative model fit" /> + </when> + </conditional> + </xml> + <xml name="branches"> - <param name="branches" type="select" label="Set of branches to test"> - <option value="All">All branches</option> - <option value="Internal">Internal branches</option> - <option value="Leaves">Leaf branches</option> - <option value="'Unlabeled-branches'">Unlabeled branches</option> - </param> + <conditional name="branch_cond"> + <param name="branch_sel" type="select" label="Set of branches to test"> + <option value="All">All branches</option> + <option value="Internal">Internal branches</option> + <option value="Leaves">Leaf branches</option> + <option value="'Unlabeled-branches'">Unlabeled branches</option> + <option value="specify">Enter a branch label</option> + </param> + <when value="specify"> + <param name="branch_label" type="text" value="Test" optional="false" label="Branch label"> + <sanitizer invalid_char=""> + <valid initial="default" /> + </sanitizer> + </param> + </when> + <when value="All" /> + <when value="Internal" /> + <when value="Leaves" /> + <when value="'Unlabeled-branches'" /> + </conditional> </xml> <xml name="citations"> <citations> @@ -114,17 +146,40 @@ <yield/> </requirements> </xml> + <xml name="alternative_model_output"> + <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json"> + <filter>advanced['save_alternative_model']</filter> + </data> + </xml> + <token name="@INPUT_TREE@"><![CDATA[ + #if $input_nhx: + --tree input.nhx + #end if + ]]> + </token> + <token name="@branch_options@"><![CDATA[ + #if $branch_cond.branch_sel == 'specify': + --branches '$branch_cond.branch_label' + #else: + --branches $branch_cond.branch_sel + #end if + ]]> + </token> + <token name="@advanced_options@"><![CDATA[ + #if $advanced.srv_options == 'specify': + --grid-size $advanced.grid_size + --starting-points $advanced.starting_points + --syn-rates $advanced.syn_rates + --rates $advanced.rates + --srv $advanced.srv + #if $advanced.save_alternative_model: + --save-fit alternative_model.json + #end if + #end if + ]]></token> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> - <token name="@CATCH_ERROR@"><![CDATA[ - EC=\$? ; - if [ \$EC -ne 0 ] ; then - if [ -f errors.log.mpinode0 ] ; then - cat errors.log.mpinode0 >&2 ; - else - cat errors.log >&2 ; - fi ; - fi ; - exit \$EC + <token name="@ERRORS@"><![CDATA[ + ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC ]]></token> <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ export HYPHY=`which hyphy` && @@ -134,11 +189,10 @@ @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token> <token name="@SYMLINK_FILES@"><![CDATA[ - ln -s '$input_file' input.$input_file.extension && - ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json && - #set $input_file = 'input.%s' % $input_file.extension - #if $input_nhx: + #if $input_nhx is not None: ln -s '$input_nhx' input.nhx && #end if + ln -s '$input_file' input.$input_file.extension && + #set $input_file = 'input.%s' % $input_file.extension ]]></token> </macros> |
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| diff -r 098451b762fb -r a4c5dc437558 test-data/busted-in2.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-in2.nex Tue Apr 27 18:03:51 2021 +0000 |
| b |
| b"@@ -0,0 +1,30 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 8;\n+\tTAXLABELS\n+\t\t'B_FR_83_HXB2' 'B_US_83_RF' 'B_US_86_JRFL' 'B_US_90_WEAU160' 'D_CD_83_ELI' 'D_CD_83_NDK' 'D_CD_84_84ZR085' 'D_UG_94_94UG114' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1320;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'B_FR_83_HXB2' CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC\n+\t'B_US_83_RF' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCATTGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCACAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAATCTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACCGGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAGCTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCATAATAGGAGCAGAAACTTTC\n+\t'B_US_86_JRFL' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCGCAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCAAAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGTGTATTATGACCCATCAAAAGAC"..b"ACTCCAATATTTGCCATAAAGAAAAAAGACAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTGAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTCAGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCACAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACCAGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAAAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGCAAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAATTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGGACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAAACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACATGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGTCAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCATAATAGGAGCAGAAACTTTC\n+\t'D_CD_84_84ZR085' CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATTGGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGACAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTAAAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTCAATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAATCTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCAAAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAAAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAATTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGCAAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAGTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGGGAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACATGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGTCAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCATAATAGGAGCAGAAACTTTC\n+\t'D_UG_94_94UG114' CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGATGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCACTAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGACAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTCAGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTAGTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCACAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACCAGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAAAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTAGGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAATTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGCGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGCAAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAAACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGGGAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGTCAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCATAGTAGGAGCAGAAACTTTC;\n+END;\n+\n+BEGIN TREES;\n+\tTREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160));\n+END;\n" |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/busted-out1.json --- a/test-data/busted-out1.json Tue Apr 20 19:55:48 2021 +0000 +++ b/test-data/busted-out1.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b'@@ -1,73 +1,73 @@\n {\n "Evidence Ratios":{\n "constrained": [\n-[1.766356514902524, 0.9484374805763239, 0.9571091930814299, 1.845676838710576, 1.513819401189324, 2.11256226458989, 7.366103227625151, 3.937756516229049, 2.586067836907899, 0.722379841928909, 0.3151239046214458, 1.502917468627881, 0.6499879033472316, 1.047489715978757, 1.060206108705189, 0.5038296392390414, 0.8532658611088545, 1.114374823999701, 0.5611409841208096, 0.6702870396165613, 0.4604115167079821, 0.3988433224622866, 2.47019807349414, 0.9858342091732886, 1.106653406611749, 1.067348070135177, 1.77412165088655, 1.321424873505688, 1.90457149631063, 0.7888758683589224, 0.7229203540914775, 0.8813401886687667, 0.6954297746421804, 4.613654710605887, 0.4975309466317643, 1.84565076502724, 0.6214894235132998, 0.9480915704528677, 0.9669462933548731, 1.488081789562878, 1.368539685217942, 1.726522735566884, 1.222915324989829, 0.7085094082639855, 0.3168181005885327, 2.290014391709923, 0.6343005734674315, 0.8841633809961478, 1.508078414734822, 2.666352901083321, 1.732923983135172, 3.102011384229053, 1.585109653073893, 3.345181824497555, 7.193115253213268, 3.850321954428519, 3.233128500312913, 1.977820966308441, 2.047653340750355, 0.6643430465826362, 3.624272911205855, 1.67814994913239, 1.752817561416471, 3.277248182160172, 0.3406457937754578, 0.4841828665456315, 1.399775481724447, 0.5510187898414104, 0.6276769404480749, 0.4535822272441153, 0.4226923979745105, 2.950051361271033, 0.9999999999999982, 1.027733519332009, 2.963278030618241, 2.8935730521221, 1.881916301985038, 0.4490192221083247, 3.102588216900087, 0.7028469232610687, 2.792137897266834, 0.3889955246330017, 0.9360790804326219, 0.4572233386404743, 2.908919410553763, 0.8995968442944373, 0.3261344314757346, 1.080257865601265, 1.399763176607792, 1.534646955858424, 0.4277164444783946, 2.361993404905034, 2.175584822495568, 3.122529901767528, 0.4453847841440882, 1.711825080925545, 0.8458710509917922, 2.741896592382772, 0.576439632416141, 1.142294357680513, 0.8086330800808955, 2.943414796294152, 0.833291758377592, 1.615921141634484, 0.7252129604805458, 2.833655116179036, 0.9138779988368123, 0.6174720822006171, 1.834532902825704, 0.2316812685220093, 2.479235579982967, 0.4643862206171616, 6.530720225707355, 0.4975309466317643, 1.158125132567293, 0.2987944638927862, 3.78696693228073, 0.7343025200073082, 1.93339742618843, 0.3642707474760721, 1.028034824972818, 1.511057897004292, 0.2969890376651506, 0.987605711796378, 0.3709886418939366, 4.185741574214752, 3.002372601666337, 0.424383367760914, 0.4658081554322532, 0.4024556436060775, 2.540164510486854, 0.5199349857684811, 0.4626485320487528, 0.9349816613814522, 0.5525607476128181, 0.5855612460554309, 1.85872747574379, 1.064964125964651, 3.177687923317396, 2.593304657270028, 5.234187858164534, 2.966427299030309, 1.920561682721974, 2.245869881969924, 3.811870935099101, 2.099654636695842, 3.369504334172069, 0.6379165155453101, 3.119867019567397, 0.9211859677702382, 2.195241379859611, 1.767535349740496, 1.225677095999665, 1.347676192394215, 1.671173168407676, 1.179430472478473, 1.873629958128968, 1.972321068578892, 1.863249013159319, 1.501711930393218, 2.85458165498371, 0.5332817404709185, 0.7514817421990073, 0.2887801591578705, 1.93925520496415, 0.2163710715496819, 2.457406602553581, 0.4895227461773333, 2.731573653164397, 0.8923840424261161, 0.6288736610053396, 3.562511382204229, 0.8043427141817341, 2.97831687935463, 3.021636055180988, 1.919432168129229, 1.231674183402057, 3.382911261347008, 1.455440822286478, 1.714894279904311, 0.4763853457361669, 0.907985271671091, 0.9191891327337078, 0.8704988461364657, 0.4660185191281315, 0.6176233729242167, 0.9987767701341157] \n+[1.751697313438667, 0.9490151622254345, 0.9575938099872893, 1.827482077500528, 1.505094606485015, 2.088346790071941, 7.070051504373732, 3.867967952992799, 2.545750919582881, 0.7247660693488289, 0.3196737937441124, 1.489449650902744, 0.6530151351740718, 1.04337285373284, 1.058333334239147, 0.5088801718500566, 0.8'..b'0.01189287130232129] \n ],\n- "Log Likelihood":-3467.004808147542,\n+ "Log Likelihood":-3467.012706765863,\n "Rate Distributions":{\n "non-synonymous/synonymous rate ratio for *test*": [\n-[0.9950576192409499, 1] \n+[0.9959842858928788, 1] \n ]\n },\n "display order":1,\n "estimated parameters":31\n },\n "Nucleotide GTR":{\n- "AIC-c":7112.85745601076,\n+ "AIC-c":7112.857310169033,\n "Equilibrium frequencies": [\n [0.3592490842490842],\n [0.181959706959707],\n [0.240018315018315],\n [0.2187728937728937] \n ],\n- "Log Likelihood":-3532.321297387654,\n+ "Log Likelihood":-3532.32122446679,\n "Rate Distributions":{\n- "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,\n+ "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,\n "Substitution rate from nucleotide A to nucleotide G":1,\n- "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,\n- "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,\n- "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,\n- "Substitution rate from nucleotide G to nucleotide T":0.304615404570875\n+ "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,\n+ "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,\n+ "Substitution rate from nucleotide G to nucleotide T":0.304509117524575\n },\n "display order":0,\n "estimated parameters":24\n },\n "Unconstrained model":{\n- "AIC-c":6910.766610587704,\n- "Log Likelihood":-3414.486640449675,\n+ "AIC-c":6910.776988890891,\n+ "Log Likelihood":-3414.491829601268,\n "Rate Distributions":{\n "Synonymous site-to-site rates":{\n "0":{\n- "proportion":0.2645541257391169,\n- "rate":0.2747941124675511\n+ "proportion":0.2655037162058198,\n+ "rate":0.2749303122566129\n },\n "1":{\n- "proportion":0.6325830460054784,\n- "rate":0.9734675888351726\n+ "proportion":0.6321791898264187,\n+ "rate":0.9740711294478059\n },\n "2":{\n- "proportion":0.1028628282554047,\n- "rate":3.028333913894314\n+ "proportion":0.1023170939677615,\n+ "rate":3.041695877803997\n }\n },\n "Test":{\n "0":{\n "omega":0,\n- "proportion":0.04809457608200497\n+ "proportion":0.386646389823596\n },\n "1":{\n- "omega":0,\n- "proportion":0.3410012743721951\n+ "omega":0.9964438830494696,\n+ "proportion":0\n },\n "2":{\n- "omega":1.89363684081788,\n- "proportion":0.6109041495458\n+ "omega":1.876622752045829,\n+ "proportion":0.613353610176404\n }\n }\n },\n@@ -341,7 +341,7 @@\n }\n },\n "input":{\n- "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",\n+ "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta",\n "number of sequences":10,\n "number of sites":187,\n "partition count":1,\n@@ -350,8 +350,8 @@\n }\n },\n "test results":{\n- "LRT":10.17362366082671,\n- "p-value":0.003088842014430382\n+ "LRT":10.17667489929045,\n+ "p-value":0.003084133210483175\n },\n "tested":{\n "0":{\n@@ -376,19 +376,19 @@\n "timers":{\n "Constrained BUSTED model fitting":{\n "order":3,\n- "timer":62\n+ "timer":70\n },\n "Overall":{\n "order":0,\n- "timer":228\n+ "timer":451\n },\n "Preliminary model fitting":{\n "order":1,\n- "timer":3\n+ "timer":10\n },\n "Unconstrained BUSTED model fitting":{\n "order":2,\n- "timer":161\n+ "timer":370\n }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/busted-out2-1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out2-1.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b'@@ -0,0 +1,338 @@\n+{\n+ "Evidence Ratios":{\n+ "constrained": [\n+[0.935557169656361, 0.9478485707814517, 0.9365713272643597, 0.9348516866501475, 0.9478485707814517, 0.9470782825238451, 0.9404255507056813, 0.9445269614625446, 0.9357171171944089, 0.9445269614625446, 0.951038343352286, 0.9642191069363555, 0.9509681609268663, 0.9357171171944089, 0.9365508162861411, 0.9330337048596494, 0.9453769311406178, 0.9354507653189286, 0.9357171171944089, 0.951038343352286, 0.944959794342383, 0.951038343352286, 0.9554450473318812, 0.957741198595587, 0.9357223141306646, 0.9635859922205572, 0.9400812190552175, 0.9471227276423632, 0.9471155585144405, 0.951038343352286, 0.9425085292914046, 0.951038343352286, 0.9382075921692818, 0.9681439336221066, 9.055411306947674, 0.9467899324264936, 0.9478485707814517, 0.9398061397692539, 1.097085569751409, 1.371682580705311, 1.704754646360477, 0.9467899324264936, 0.9509681609268663, 0.9467899324264936, 0.9364415899930733, 0.951038343352286, 0.9478485707814517, 0.9525827524658199, 1.146813959542357, 0.9478485707814517, 0.9362276370626634, 0.9348516866501475, 0.9467899324264936, 0.9486832156560699, 0.9357171171944089, 0.9541686971206805, 0.9484511531422709, 0.9404255507056813, 0.9357171171944089, 1.072863229391129, 0.947891315956519, 0.938167627826613, 0.9425085292914046, 0.9509681609268663, 0.951038343352286, 0.9514408733975561, 0.9395660064639854, 0.9365128450433999, 0.9404014893688138, 0.9514344449206511, 0.957741198595587, 0.9388792918800136, 0.951038343352286, 0.9642191069363555, 0.9445269614625446, 0.9453769311406178, 0.9418928080136506, 0.9388792918800136, 0.9467899324264936, 0.9399880829471382, 0.9484511531422709, 0.9509681609268663, 1.153990916133998, 0.9404255507056813, 0.9554450473318812, 0.9412338215355154, 0.942333955072914, 0.957741198595587, 0.9470815762343416, 0.9449667231570663, 0.9557119925844111, 0.9676532717080474, 0.9365050172103501, 0.9425085292914046, 0.9357012899378949, 0.9407207493748144, 0.9348483936808639, 1.953541836729934, 0.9362670029301522, 0.9644232801771531, 0.9515108647313498, 0.9509681609268663, 1.168382764503998, 0.9515108647313498, 0.949860271872106, 1.047791522454514, 0.9400812190552175, 0.9445269614625446, 0.9566068656126535, 0.9453769311406178, 0.9434809129833114, 0.936045980720387, 0.9455636023716772, 0.9382075921692818, 0.9549292932384192, 0.9479532753114727, 0.949860271872106, 1.071924199060109, 0.9347728559684337, 0.9642191069363555, 61.30480048708166, 1.392589724214399, 1.068829280572215, 0.9452448851782124, 0.9383322213205718, 0.9520356968106081, 0.9548771157697881, 0.9403109573428395, 0.9383425168225155, 0.9481200597562297, 0.9401597754529221, 0.9425085292914046, 1.081655864332756, 0.9365128450433999, 0.958884569235499, 0.9416389648192759, 0.9484511531422709, 0.9474364959906919, 0.9400812190552175, 0.9357171171944089, 1.013189964747481, 0.9478485707814517, 0.939061940389555, 0.9549292932384192, 0.9544426850176303, 0.9541087300514087, 0.9484511531422709, 0.9456450378925056, 0.9399863915898927, 0.9357147779844784, 0.9552428339477506, 0.9365032950653777, 0.957741198595587, 0.951038343352286, 0.9364880871021735, 0.949860271872106, 0.9357012899378949, 0.9382075921692818, 0.9425085292914046, 0.9418928080136506, 0.9554450473318812, 0.9365128450433999, 0.9333687495168144, 0.9330337048596494, 1.030183566875361, 0.951038343352286, 0.9530190340820841, 0.9642191069363555, 0.9471668565289959, 0.9348308160631009, 0.947891315956519, 1.060517303033454, 0.951038343352286, 0.9554450473318812, 0.9484511531422709, 0.9357171171944089, 1.428578774814407, 1.256482256153546, 1.21301128797193, 0.9447052888159178, 0.9549292932384192, 0.9554450473318812, 0.9541087300514087, 0.9330337048596494, 0.9453769311406178, 0.9453769311406178, 0.9635859922205572, 0.9549292932384192, 0.9445269614625446, 0.9364880871021735, 0.9422504512769631, 0.9408248422372665, 0.9642191069363555, 0.9471081975229871, 0.9425085292914046, 0.9362670029301522, 0.9544426850176303, 0.9407207493748144, 0.9390630876730207,'..b'6807635995],\n+ [0.01505600521072376],\n+ [0.002882972930821469],\n+ [0.005825499564956559],\n+ [0.005903516300053625],\n+ [0.02274367484777162],\n+ [0.004355032959661065],\n+ [0.008800028033786655],\n+ [0.008917880494044083],\n+ [0.06143704799998004],\n+ [0.01176416611541591],\n+ [0.0237713451467977],\n+ [0.0240896977132239],\n+ [0.0262463496652457],\n+ [0.005025736545566795],\n+ [0.01015528996016046],\n+ [0.01029129247081581],\n+ [0.02256567087217255],\n+ [0.004320948178469224],\n+ [0.008731154380523415],\n+ [0.00884808446536876],\n+ [0.034087812394816],\n+ [0.006527245376826684],\n+ [0.01318932435908579],\n+ [0.01336595951511979],\n+ [0.01178447449308153],\n+ [0.02413128354890585],\n+ [0.0262916585104385],\n+ [0.005034412430862358],\n+ [0.01017282094890981],\n+ [0.01030905823951665],\n+ [0.004328407393735399],\n+ [0.008746226896405704],\n+ [0.008863358836639712],\n+ [0.03414665788893068],\n+ [0.006538513303760755],\n+ [0.0132120929750345],\n+ [0.01338903305480236] \n+ ],\n+ "Log Likelihood":-3176.217093030587,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.231720664913378, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":28\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":6683.094244259512,\n+ "Equilibrium frequencies": [\n+[0.4044507575757576],\n+ [0.1662878787878788],\n+ [0.2095643939393939],\n+ [0.2196969696969697] \n+ ],\n+ "Log Likelihood":-3320.503280793639,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,\n+ "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,\n+ "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,\n+ "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568\n+ },\n+ "display order":0,\n+ "estimated parameters":21\n+ },\n+ "Unconstrained model":{\n+ "AIC-c":6391.938375474656,\n+ "Log Likelihood":-3163.666348620609,\n+ "Rate Distributions":{\n+ "Test":{\n+ "0":{\n+ "omega":0.1490485393860332,\n+ "proportion":0.02658974082564446\n+ },\n+ "1":{\n+ "omega":0.169565784922581,\n+ "proportion":0.9641001770967245\n+ },\n+ "2":{\n+ "omega":15.09387961636913,\n+ "proportion":0.009310082077631076\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":32\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex",\n+ "number of sequences":8,\n+ "number of sites":440,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"\n+ }\n+ },\n+ "test results":{\n+ "LRT":8.711160142067456,\n+ "p-value":0.006417496108925114\n+ },\n+ "tested":{\n+ "0":{\n+ "B_FR_83_HXB2":"test",\n+ "B_US_83_RF":"test",\n+ "B_US_86_JRFL":"test",\n+ "B_US_90_WEAU160":"test",\n+ "D_CD_83_ELI":"test",\n+ "D_CD_83_NDK":"test",\n+ "D_CD_84_84ZR085":"test",\n+ "D_UG_94_94UG114":"test",\n+ "Node1":"test",\n+ "Node10":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node9":"test"\n+ }\n+ },\n+ "timers":{\n+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":23\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":133\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":4\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":105\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/busted-out2-2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out2-2.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b"@@ -0,0 +1,1730 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 8;\n+\tTAXLABELS\n+\t\t'B_FR_83_HXB2' 'B_US_83_RF' 'B_US_86_JRFL' 'B_US_90_WEAU160' 'D_CD_83_ELI' 'D_CD_83_NDK' 'D_CD_84_84ZR085' 'D_UG_94_94UG114' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1320;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'B_FR_83_HXB2' CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC\n+\t'B_US_83_RF' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCATTGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCACAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAATCTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACCGGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAGCTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCATAATAGGAGCAGAAACTTTC\n+\t'B_US_86_JRFL' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCGCAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCAAAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGTGTATTATGACCCATCAAAAGACT"..b'nt_3[60][31]:=0.1712746635706107*t*busted.test.theta_CT*busted.test.omega3;\n+busted.test_Q_component_3[60][47]:=0.2567033972679326*t*busted.test.theta_GT*busted.test.omega3;\n+busted.test_Q_component_3[60][49]:=0.4256503784977386*t*busted.test.theta_AT*busted.test.omega3;\n+busted.test_Q_component_3[60][53]:=0.1818409092376876*t*busted.test.theta_CT*busted.test.omega3;\n+busted.test_Q_component_3[60][56]:=0.1563402972714242*t*busted.test.theta_GT*busted.test.omega3;\n+busted.test_Q_component_3[60][57]:=0.5074830879161225*t*busted.test.theta_AT*busted.test.omega3;\n+busted.test_Q_component_3[60][58]:=0.09717451507454297*t*busted.test.theta_CT;\n+busted.test_Q_component_3[60][59]:=0.1963563685387479*t*busted.test.theta_GT*busted.test.omega3;\n+\n+\n+busted.test_pi={\n+{0.07535940345366139} \n+{0.01443006409728228} \n+{0.02915821068672351} \n+{0.02954870567752823} \n+{0.03219408024958758} \n+{0.006164627375802654} \n+{0.01245659774045292} \n+{0.01262342001471309} \n+{0.0276793164843978} \n+{0.005300125700761717} \n+{0.01070973633984303} \n+{0.01085316415297191} \n+{0.0418125103783387} \n+{0.008006395714089126} \n+{0.01617817990958604} \n+{0.0163948426631036} \n+{0.0409913146415633} \n+{0.007849150478922548} \n+{0.01586044121725868} \n+{0.01607284872448998} \n+{0.01751178502783737} \n+{0.003353213651232053} \n+{0.006775694789785172} \n+{0.006866436807635995} \n+{0.01505600521072376} \n+{0.002882972930821469} \n+{0.005825499564956559} \n+{0.005903516300053625} \n+{0.02274367484777162} \n+{0.004355032959661065} \n+{0.008800028033786655} \n+{0.008917880494044083} \n+{0.06143704799998004} \n+{0.01176416611541591} \n+{0.0237713451467977} \n+{0.0240896977132239} \n+{0.0262463496652457} \n+{0.005025736545566795} \n+{0.01015528996016046} \n+{0.01029129247081581} \n+{0.02256567087217255} \n+{0.004320948178469224} \n+{0.008731154380523415} \n+{0.00884808446536876} \n+{0.034087812394816} \n+{0.006527245376826684} \n+{0.01318932435908579} \n+{0.01336595951511979} \n+{0.01178447449308153} \n+{0.02413128354890585} \n+{0.0262916585104385} \n+{0.005034412430862358} \n+{0.01017282094890981} \n+{0.01030905823951665} \n+{0.004328407393735399} \n+{0.008746226896405704} \n+{0.008863358836639712} \n+{0.03414665788893068} \n+{0.006538513303760755} \n+{0.0132120929750345} \n+{0.01338903305480236} \n+};\n+Model busted.test=(\'Exp(busted.test_Q_component_1)*1*busted.test.bsrel_mixture_aux_0+Exp(busted.test_Q_component_2)*1*(1-busted.test.bsrel_mixture_aux_0)*busted.test.bsrel_mixture_aux_1+Exp(busted.test_Q_component_3)*1*(1-busted.test.bsrel_mixture_aux_0)*(1-busted.test.bsrel_mixture_aux_1)\',busted.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n+TRY_NUMERIC_SEQUENCE_MATCH=0;\n+ACCEPT_ROOTED_TREES=0;\n+\n+UseModel (busted.test);\n+Tree cuWdXMfP.tree_id_0=((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9);\n+\n+cuWdXMfP.tree_id_0.D_CD_83_ELI.t=0.1377903766097694;\n+cuWdXMfP.tree_id_0.D_CD_83_NDK.t=0.06607109645594529;\n+cuWdXMfP.tree_id_0.Node3.t=0.0890081009446355;\n+cuWdXMfP.tree_id_0.D_UG_94_94UG114.t=0.4322474154485661;\n+cuWdXMfP.tree_id_0.Node2.t=0.01436667144151429;\n+cuWdXMfP.tree_id_0.D_CD_84_84ZR085.t=0.2152052309993384;\n+cuWdXMfP.tree_id_0.Node1.t=0.1867555551194544;\n+cuWdXMfP.tree_id_0.B_US_83_RF.t=0.2093873697545922;\n+cuWdXMfP.tree_id_0.B_FR_83_HXB2.t=0.08552069057797769;\n+cuWdXMfP.tree_id_0.B_US_86_JRFL.t=0.1313117411090917;\n+cuWdXMfP.tree_id_0.Node10.t=0.01181372524396516;\n+cuWdXMfP.tree_id_0.B_US_90_WEAU160.t=0.1600546391700751;\n+cuWdXMfP.tree_id_0.Node9.t=0.03506352054252541;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n+SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n+\n+DataSet busted.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n+DataSetFilter busted.filter.default = CreateFilter(busted.codon_data,3,"0-1319","4,5,7,6,1,0,2,3","TAA,TAG,TGA");\n+ASSUME_REVERSIBLE_MODELS=1;\n+USE_LAST_RESULTS=0;\n+LikelihoodFunction cuWdXMfP.likelihoodFunction = (busted.filter.default,cuWdXMfP.tree_id_0);\n+\n+END;\n\\ No newline at end of file\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/gard-out1.json --- a/test-data/gard-out1.json Tue Apr 20 19:55:48 2021 +0000 +++ b/test-data/gard-out1.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b'@@ -3,316 +3,53 @@\n "authors":"Sergei L Kosakovsky Pond",\n "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891\xe2\x80\x931901",\n "contact":"spond@temple.edu",\n- "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\\n approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\\n incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\\n placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\\n tests run to distinguish topological incongruence from rate-variation.",\n+ "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\\n approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\\n incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\\n placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\\n tests run to distinguish topological incongruence from rate-variation. v0.2 adds and spooling results to JSON after each breakpoint search conclusion",\n "requirements":"A sequence alignment.",\n- "version":"0.1"\n+ "version":"0.2"\n },\n- "baselineScore":8884.998566352424,\n+ "baselineScore":1450.968340148184,\n+ "bestModelAICc":1450.968340148184,\n "breakpointData":{\n- "0":{\n- "bps": [\n-[1, 461] \n- ],\n- "tree":"(((((((TREESPARROW_HENAN_1_2004:0.01973996359641645,TREESPARROW_HENAN_2_2004:0)Node6:0.006601594605919903,CHICKEN_HEBEI_326_2005:0.02877904543700591)Node5:0.002960697265622527,SWINE_ANHUI_2004:0.01220336915594569)Node4:0.004301817483024902,((DUCK_GUANGZHOU_20_2005:0.006496379151101181,(GOOSE_SHANTOU_2216_2005:0.008666763019733412,PEREGRINEFALCON_HK_D0028_2004:0.006494907750172948)Node14:0)Node12:0.006529386248252737,CK_HK_WF157_2003:0.008749819170042668)Node11:0.006517868346508392)Node3:0.004369843971142481,((TREESPARROW_HENAN_3_2004:0.004310725480928182,((CHICKEN_HONGKONG_915_97:0,(HONGKONG_97_98:0.007234718327388172,HONGKONG_538_97:0)Node24:0)Node22:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node27:0.002160209380619512)Node21:0.02651640051975179)Node19:0.002209468499615626,TREESPARROW_HENAN_4_2004:0.008707376458939551)Node18:0)Node2:0.01527162191938894,MALLARD_VIETNAM_16_2003:0.00216300836609909)Node1:0,HUMAN_VIETNAM_CL105_2005:0.01089634139979296,(((DUCK_VIETNAM_376_2005:0.002165747961920766,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.01092964139649115)Node35:0.002165571630784742,VIETNAM_3062_2004:0)Node34:0.002160659783816526,DUCK_VIETNAM_272_2005:0.006501625005083654)Node33:0)"\n- },\n- "1":{\n- "bps": [\n-[462, 650] \n- ],\n- "tree":"((((((TREESPARROW_HENAN_1_2004:0,TREESPARROW_HENAN_3_2004:0.01064277225673711)Node5:0.00531987705161906,TREESPARROW_HENAN_2_2004:0)Node4:0.005231591103466107,CHICKEN_HEBEI_326_2005:0.05043188754547531)Node3:0.005435427857192481,CK_HK_WF157_2003:0)Node2:0.005367407450692448,((TREESPARROW_HENAN_4_2004:0.005403333058615208,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node18:0.005303893633648769)Node16:0,HONGKONG_97_98:0)Node15:0,HONGKONG_538_97:0)Node14:0.0160450339521957)Node12:0.01065583332597595,((DUCK_GUANGZHOU_20_2005:0.02156617952480121,GOOSE_SHANTOU_2216_2005:0.005315754078746889)Node24:0,PEREGRINEFALCON_HK_D0028_2004:0.005310132566451705)Node23:0)Node11:0.005324661683629481)Node1:0.01075596871747344,(SWINE_ANHUI_2004:0.01612941661930485,DUCK_VIETNAM_272_2005:0.005332918418299072)Node28:0.005343017103483476,((HUMAN_VIETNAM_CL105_2005:0.01615610619083483,DUCK_VIETNAM_376_2005:0.01622595235090508)Node32:0.005403715853761346,(VI'..b'326_2005:0.05043188754547531)Node3:0.005435427857192481,CK_HK_WF157_2003:0)Node2:0.005367407450692448,((TREESPARROW_HENAN_4_2004:0.005403333058615208,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node18:0.005303893633648769)Node16:0,HONGKONG_97_98:0)Node15:0,HONGKONG_538_97:0)Node14:0.0160450339521957)Node12:0.01065583332597595,((DUCK_GUANGZHOU_20_2005:0.02156617952480121,GOOSE_SHANTOU_2216_2005:0.005315754078746889)Node24:0,PEREGRINEFALCON_HK_D0028_2004:0.005310132566451705)Node23:0)Node11:0.005324661683629481)Node1:0.01075596871747344,(SWINE_ANHUI_2004:0.01612941661930485,DUCK_VIETNAM_272_2005:0.005332918418299072)Node28:0.005343017103483476,((HUMAN_VIETNAM_CL105_2005:0.01615610619083483,DUCK_VIETNAM_376_2005:0.01622595235090508)Node32:0.005403715853761346,(VIETNAM_3062_2004:0,(MALLARD_VIETNAM_16_2003:0.01066500623689393,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0)Node37:0.005316372444723995)Node35:0)Node31:0)"\n- },\n- "2":{\n- "newickString":"(((((((TREESPARROW_HENAN_1_2004:0.001954008187578416,TREESPARROW_HENAN_3_2004:0.003896316686452931)Node6:0.001938506890703636,TREESPARROW_HENAN_4_2004:0)Node5:0.005890390504717593,((CHICKEN_HEBEI_326_2005:0.0118071209154035,(SWINE_ANHUI_2004:0,TREESPARROW_HENAN_2_2004:0.001939618450410721)Node13:0.01383276182388132)Node11:0.009974147725569997,((CHICKEN_HONGKONG_915_97:0,GOOSE_HONGKONG_W355_97:0)Node17:0.001941847153562197,((DUCK_HONGKONG_Y283_97:0,HONGKONG_538_97:0)Node21:0,HONGKONG_97_98:0.005840445012127324)Node20:0.001942715072940801)Node16:0.01987446960589405)Node10:0.005913850464875198)Node4:0.005886750382502456,(((DUCK_GUANGZHOU_20_2005:0.003893604042162395,GOOSE_SHANTOU_2216_2005:0.003905435534305824)Node27:0.001941929040845811,PEREGRINEFALCON_HK_D0028_2004:0.003899037680959845)Node26:0.001951590047476092,CK_HK_WF157_2003:0.005864286435734769)Node25:0.001925781157666145)Node3:0.009803928769016717,DUCK_VIETNAM_272_2005:0.01580156952635168)Node2:0,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.003890598353658968)Node1:0,((HUMAN_VIETNAM_CL105_2005:0.003905371265795895,DUCK_VIETNAM_376_2005:0.0137665342243657)Node35:0.001932867193851192,MALLARD_VIETNAM_16_2003:0.003887459835724038)Node34:0,VIETNAM_3062_2004:0.00194102772512571)"\n- },\n- "3":{\n- "newickString":"(TREESPARROW_HENAN_1_2004:0,((TREESPARROW_HENAN_3_2004:0.005713571370335148,TREESPARROW_HENAN_4_2004:0)Node3:0.00189607429178233,(CHICKEN_HEBEI_326_2005:0.005712316903324198,(SWINE_ANHUI_2004:0.005701998731046575,(((CHICKEN_HONGKONG_915_97:0,HONGKONG_97_98:0)Node12:0.001895621658683188,(GOOSE_HONGKONG_W355_97:0,HONGKONG_538_97:0)Node15:0)Node11:0.01534803500036186,((DUCK_HONGKONG_Y283_97:0.0001941011375241317,(((HUMAN_VIETNAM_CL105_2005:0.001928158212296621,DUCK_VIETNAM_376_2005:0.003824815472812549)Node23:0.001900556734363341,(VIETNAM_3062_2004:0.001945118440015516,MALLARD_VIETNAM_16_2003:0)Node26:0)Node22:0,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00380825293990655,DUCK_VIETNAM_272_2005:0.005749159769097136)Node29:0.001884324589239026)Node21:0.006136201619836659)Node19:0.006956231732180768,(((DUCK_GUANGZHOU_20_2005:0.003782134609270667,GOOSE_SHANTOU_2216_2005:0.005745814969410696)Node34:0.005728903718080784,PEREGRINEFALCON_HK_D0028_2004:0)Node33:0.001883474579815808,CK_HK_WF157_2003:0.005783922057126199)Node32:0.003686703559509533)Node18:0.002359028413665987)Node10:0.003781653021946557)Node8:0.003836413220384994)Node6:0.001894177236914572)Node2:0,TREESPARROW_HENAN_2_2004:0.00767492225272676)"\n- }\n+ "newickString":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)"\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/gard-out1.nex --- a/test-data/gard-out1.nex Tue Apr 20 19:55:48 2021 +0000 +++ b/test-data/gard-out1.nex Tue Apr 27 18:03:51 2021 +0000 |
| b |
| @@ -0,0 +1,37 @@ +#NEXUS + +BEGIN TAXA; + DIMENSIONS NTAX = 12; + TAXLABELS + 'BRO1_1' 'BRO2' 'BRO3_1' 'BRO4' 'BRO5' 'BRO6' 'BRO7_1' 'BRO9' 'BRO10' 'BRO11_1' 'BRO12' 'BRO8' ; +END; + +BEGIN CHARACTERS; + DIMENSIONS NCHAR = 428; + FORMAT + DATATYPE = DNA + GAP=- + MISSING=? + ; + +MATRIX + 'BRO1_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO2' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACCCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTGCATAAAGCCATTTACCGTACATAGCACATTATA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO3_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAGCTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO4' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO5' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO6' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO7_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO9' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO10' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO11_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACTACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO12' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGACTACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO8' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC; +END; + +BEGIN ASSUMPTIONS; + CHARSET span_1 = 1-428; +END; +BEGIN TREES; + TREE tree_1 = (((BRO1_1:1e-10,BRO2:0.007446048662499141)Node2:1.699082282683926e-05,(((BRO5:0.002291051777868712,(BRO6:0.004965711012353363,BRO7_1:1e-10)Node9:0.0001955595843124865)Node7:0.002191267352110732,(BRO9:0.004469023573866088,((BRO10:0.002870586428367251,BRO11_1:0.01462820627459318)Node15:0.001454707803761366,BRO12:0.006027959855484483)Node14:0.005661145911839864)Node12:0.0003039715029625697)Node6:0.0002803682303139691,BRO8:0.002464847898104024)Node5:1.386828770154629e-05)Node1:3.347353150116037e-06,BRO3_1:0.002467834453766899,BRO4:0.002462875913900023); +END; |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/relax-in2.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nex Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b"@@ -0,0 +1,86 @@\n+#NEXUS\n+\n+[\n+Generated by HYPHY 0.9920070619beta(MP) for MacOS(Carbon) on Thu Jun 21 16:59:04 2007\n+\n+]\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 10;\n+\tTAXLABELS\n+\t\t'Human' 'Chimp' 'Baboon' 'RhMonkey' 'Cow' 'Pig' 'Horse' 'Cat' 'Mouse' 'Rat' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 561;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'Human' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'Chimp' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'Baboon' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'RhMonkey' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'Cow' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT\n+\t'Pig' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT\n+\t'Horse' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGA"..b'GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC\n+\t\'Mouse\' ---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC\n+\t\'Rat\' ---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC;\n+END;\n+\n+BEGIN TREES;\n+\tTREE tree = ((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey{PR}:0.002015,Baboon{PR}:0.003108){PR}:0.022733,(Human{PR}:0.004349,Chimp{PR}:0.000799){PR}:0.011873){PR}:0.101856){PR}:0.340802,Rat:0.050958,Mouse:0.097950);\n+END;\n+\n+BEGIN HYPHY;\n+\n+DATA_PANEL_SOURCE_PATH="";\n+DataSet CD2 = ReadDataFile (USE_NEXUS_FILE_DATA);\n+DataSetFilter CD2_part = CreateFilter (CD2,3,"0-560","(null)","TAA,TAG,TGA");\n+Tree CD2_tree=((((Pig,Cow)Node3,Horse,Cat)Node2,((RhMonkey,Baboon)Node9,(Human,Chimp)Node12)Node8)Node1,Rat,Mouse);\n+OpenDataPanel(CD2,"(null)","0,0,0,0,2,0,10","MG94xREV_3x4,6,0,14443523,CD2_tree",CD2_LF);\n+\n+global CD2_part_Shared_AC=0.5710714109234631;\n+global CD2_part_Shared_AT=0.2756961373814887;\n+global CD2_part_Shared_CG=0.4456308760366715;\n+global CD2_part_Shared_CT=0.9454291760502562;\n+global CD2_part_Shared_GT=0.3224080259059006;\n+CD2_tree.Node12.synRate=0.08168540352543764;\n+CD2_tree.Node8.nonSynRate=0.2938890030949185;\n+CD2_tree.Human.synRate=1e-30;\n+CD2_tree.Baboon.nonSynRate=0;\n+CD2_tree.Baboon.synRate=0.01716650886630832;\n+CD2_tree.Node12.nonSynRate=0.02962786133931161;\n+CD2_tree.Chimp.synRate=1e-30;\n+CD2_tree.Chimp.nonSynRate=0.005834136861061837;\n+CD2_tree.Node9.nonSynRate=0.0433794394076959;\n+CD2_tree.Human.nonSynRate=0;\n+CD2_tree.Node9.synRate=0.1139808847086709;\n+CD2_tree.Node8.synRate=0.1586154947684889;\n+CD2_tree.Rat.synRate=0.1533251749656354;\n+CD2_tree.Mouse.nonSynRate=0.2332402459120736;\n+CD2_tree.Mouse.synRate=0.4604267094040578;\n+CD2_tree.Rat.nonSynRate=0.1585006932449144;\n+CD2_tree.Node1.nonSynRate=0.5097883291072822;\n+CD2_tree.Node1.synRate=1.227004762734591;\n+CD2_tree.RhMonkey.synRate=0;\n+CD2_tree.Node3.synRate=0.1877287558837553;\n+CD2_tree.Pig.nonSynRate=0.4826366809736332;\n+CD2_tree.Horse.nonSynRate=0.518627673056701;\n+CD2_tree.Cow.nonSynRate=0.681831503936737;\n+CD2_tree.Cat.synRate=0.4672127128189641;\n+CD2_tree.Node3.nonSynRate=0.2648957141533021;\n+CD2_tree.Horse.synRate=0.430860769501357;\n+CD2_tree.Pig.synRate=0.3721230153643161;\n+CD2_tree.Node2.synRate=0.2137858662796737;\n+CD2_tree.RhMonkey.nonSynRate=0.01161863878954486;\n+CD2_tree.Cat.nonSynRate=0.7203773170684773;\n+CD2_tree.Node2.nonSynRate=0.1379570235930709;\n+CD2_tree.Cow.synRate=0.3646221318370894;\n+\n+END;\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/relax-out1.json --- a/test-data/relax-out1.json Tue Apr 20 19:55:48 2021 +0000 +++ b/test-data/relax-out1.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b'@@ -1,486 +1,174 @@\n {\n- "analysis":{\n- "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of \'Test\' branches evolves under relaxed selection relative to a set of \'Reference\' branches (R), as measured by the relaxation parameter (K).\\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems",\n- "version":"2.1",\n- "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",\n- "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",\n- "contact":"spond@temple.edu",\n- "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"\n- },\n- "input":{\n- "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa",\n- "number of sequences":10,\n- "number of sites":187,\n- "partition count":1,\n- "trees":{\n- "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n- }\n- },\n- "fits":{\n- "Nucleotide GTR":{\n- "Log Likelihood":-3531.964032193222,\n- "estimated parameters":24,\n- "AIC-c":7112.142925621896,\n- "Equilibrium frequencies":[\n- [0.3563279857397504],\n- [0.1837789661319073],\n- [0.2402852049910873],\n- [0.2196078431372549]\n- ],\n- "Rate Distributions":{\n- "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838,\n- "Substitution rate from nucleotide A to nucleotide G":1,\n- "Substitution rate from nucleotide A to nucleotide T":0.264131123736109,\n- "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388,\n- "Substitution rate from nucleotide C to nucleotide T":1.017887589835735,\n- "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065\n- },\n- "display order":0\n- },\n- "MG94xREV with separate rates for branch sets":{\n- "Log Likelihood":-3460.931903299487,\n- "estimated parameters":32,\n- "AIC-c":6987.013507197776,\n- "Equilibrium frequencies":[\n- [0.04785168648208005],\n- [0.03911346079312019],\n- [0.04842054060317301],\n- [0.04069665666515385],\n- [0.01817010744778396],\n- [0.01485205303123071],\n- [0.01838611113045968],\n- [0.01545321970309948],\n- [0.0190138898893362],\n- [0.01554175184587827],\n- [0.01923992433904378],\n- [0.01617083546230154],\n- [0.02796925133965702],\n- [0.02286176927319543],\n- [0.02830174586718859],\n- [0.02378714529482007],\n- [0.01687870337957799],\n- [0.01379647304851128],\n- [0.01707935503225849],\n- [0.01435491300079667],\n- [0.006409133648843443],\n- [0.005238757839512795],\n- [0.006485324528555602],\n- [0.005450807083377185],\n- [0.006706760641638982],\n- [0.005482034985409045],\n- [0.006786489669196017],\n- [0.005703931360295163],\n- [0.009865581170012171],\n- [0.008064021368173151],\n- [0.009982861811889655],\n- [0.008390428826966174],\n- [0.03287895020631181],\n- [0.02687490503171972],\n- [0.033269810543681],\n- [0.0279627207822247],\n- [0.01248470225271473],\n- [0.01020486315060615],\n- [0.01263311863778268],\n- [0.01061792547971484],\n- [0.01306446616325414],\n- [0.01067875601941112],\n- [0.01321977470017749],\n- [0.01111100011404158],\n- [0.01921770557551369],\n- [0.01570834862514353],\n- [0.01944616295744266],\n- [0.01634417558076203],\n- [0.01975257768318274],\n- [0.02055210293142003],\n- [0.00917603432671'..b' "omega":2.19971015101232,\n+ "proportion":0.4620912608347691\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":1.054840660215593e-44,\n+ "proportion":0.4504132080156107\n+ },\n+ "1":{\n+ "omega":1.054840660215593e-44,\n+ "proportion":0.08749553114962015\n+ },\n+ "2":{\n+ "omega":6.350765030542244,\n+ "proportion":0.4620912608347691\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":36\n+ },\n+ "RELAX null":{\n+ "AIC-c":6946.046672507471,\n+ "Log Likelihood":-3437.336313352972,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0.1150006822953211,\n+ "proportion":0.542405144031307\n+ },\n+ "1":{\n+ "omega":0.2401508033814633,\n+ "proportion":0.08223353569636478\n+ },\n+ "2":{\n+ "omega":3.69263720947284,\n+ "proportion":0.3753613202723282\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0.1150006822953211,\n+ "proportion":0.542405144031307\n+ },\n+ "1":{\n+ "omega":0.2401508033814633,\n+ "proportion":0.08223353569636478\n+ },\n+ "2":{\n+ "omega":3.69263720947284,\n+ "proportion":0.3753613202723282\n+ }\n+ }\n+ },\n+ "display order":3,\n+ "estimated parameters":35\n+ },\n+ "RELAX partitioned descriptive":{\n+ "AIC-c":6937.04707353565,\n+ "Log Likelihood":-3427.626871923648,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0.1943306885168281,\n+ "proportion":0.3359458135547653\n+ },\n+ "1":{\n+ "omega":0.2607558478587815,\n+ "proportion":0.4332550437039296\n+ },\n+ "2":{\n+ "omega":4.134271224300374,\n+ "proportion":0.2307991427413052\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.4753488415962343\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.03858318603767072\n+ },\n+ "2":{\n+ "omega":6.017221959238516,\n+ "proportion":0.486067972366095\n+ }\n+ }\n+ },\n+ "display order":5,\n+ "estimated parameters":40\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "test results":{\n+ "LRT":16.20300116404087,\n+ "p-value":5.690389451429301e-05,\n+ "relaxation or intensification parameter":2.344938789085876\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"Reference",\n+ "Cat":"Test",\n+ "Chimp":"Reference",\n+ "Cow":"Test",\n+ "Horse":"Test",\n+ "Human":"Reference",\n+ "Mouse":"Reference",\n+ "Node1":"Reference",\n+ "Node12":"Reference",\n+ "Node2":"Reference",\n+ "Node3":"Reference",\n+ "Node8":"Reference",\n+ "Node9":"Reference",\n+ "Pig":"Reference",\n+ "Rat":"Reference",\n+ "RhMonkey":"Reference"\n+ }\n+ },\n+ "timers":{\n+ "General descriptive model fitting":{\n+ "order":2,\n+ "timer":132\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":324\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":8\n+ },\n+ "RELAX alternative model fitting":{\n+ "order":3,\n+ "timer":65\n+ },\n+ "RELAX null model fitting":{\n+ "order":4,\n+ "timer":66\n+ },\n+ "RELAX partitioned descriptive":{\n+ "order":5,\n+ "timer":53\n+ }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/relax-out2-1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out2-1.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b'@@ -0,0 +1,525 @@\n+{\n+ "Synonymous site-posteriors": [\n+[0.2717348381268465, 0.5635158143073038, 0.5580958985234344, 0.4419267392327456, 0.1775513314393873, 0.01303903284026798, 0.00125071980641974, 0.2376006215377312, 0.8837687913991302, 0.697488732253998, 0.76440666757549, 0.1859131352278527, 0.4676839084660329, 0.5320161033357819, 0.4513687349306337, 0.8514990846254493, 0.9101555767748879, 0.9112112654445478, 0.9624478616388369, 0.9472735837633918, 0.8715894173292342, 0.9248557783401865, 0.3852870058193366, 0.7504386709677574, 0.7275694213063354, 0.1979029930878776, 0.2585255313006612, 0.426812371619399, 0.03564414482172501, 0.3292941826787388, 0.1427864928730872, 0.8324822227281018, 0.9311167984186458, 0.1209539167468769, 0.8726642109588801, 1.798577785061191e-05, 0.584102863529593, 0.5747348035616634, 0.5814406651776627, 0.02251840852563282, 0.1607002230623373, 0.499402751628698, 0.9327364905381349, 0.1164578922551683, 0.7414294602970922, 0.04004321943657974, 0.1252919499200681, 0.7016909689123084, 0.3099147090319344, 0.1594271385761372, 0.001721088532959928, 0.0002106542138058178, 0.7670245595319366, 0.01765606757145387, 0.08528617939935416, 0.01185048796937841, 0.008218049898468071, 0.294285815926654, 0.4088819101657737, 0.1819814701794264, 0.06741006997792491, 0.1648869485561294, 0.6641637464726119, 0.1696421815033135, 0.5337345685031449, 0.9785329157950278, 0.6089117121305408, 0.9214198863478258, 0.7040511824729966, 0.8748810706893103, 0.7603207301908244, 0.1587648197710778, 0.28009015626025, 0.9473769917649164, 0.03667497185975328, 0.6646432746680839, 0.005707942217110617, 0.4172795698582943, 0.002426641321239203, 0.9036479890682162, 0.8165937919459629, 0.5380686752231248, 0.8348947378138256, 0.8825623566861087, 0.003194607014896987, 0.1034323185116836, 0.1251183560640448, 0.6731739154042389, 0.02049494631105097, 0.7272701824195644, 0.9376578101739967, 0.03161216349993828, 0.08060038603464466, 0.05713766811791781, 0.7236799166647727, 0.03049686563145122, 0.4831167820690108, 0.3259152163804719, 0.9355990871535625, 0.2598255955335131, 0.649043721535527, 0.1395744847880144, 0.8655465087299661, 0.5535165112383126, 0.8759601400318501, 0.1331847979385494, 0.9385179832315519, 0.9590294197009215, 0.1177725177949566, 0.5310119897564728, 0.04436932195281112, 0.877273324169318, 0.07309972300058731, 0.8726642109588801, 0.0823189228969842, 0.674523501474146, 0.4093792912564727, 0.8837869026711356, 0.1208432028324516, 0.7875716367935024, 0.9342090047974666, 0.7281976470761374, 0.6335560301454017, 0.2642816632435872, 0.7601746562441594, 0.3971532429331721, 0.07967254820654134, 0.9205611063156326, 0.4126590346311199, 0.4718488374006657, 0.2324587146851173, 0.2530879180545083, 0.6735650752750825, 0.6778765556227805, 0.9393601651000962, 0.1757530496502532, 0.3931715696771638, 0.7913247469383754, 0.05849180455884406, 0.007027787474985664, 0.002980098295172601, 0.188566078048928, 0.02837364230845984, 0.008078062694748547, 0.4539148488391334, 0.2698860362225194, 0.03514662617223248, 0.8484422182215356, 0.5225500090930265, 0.8755046006217432, 0.01843684138990366, 0.6656855504934923, 0.7055653078864003, 0.236066638653311, 0.1567944657161159, 0.8781825877891227, 0.4362059051173987, 0.163327088806649, 0.004489982631214889, 0.03278376720971195, 0.03145887036879619, 0.6158371404365816, 0.8645373560796752, 0.6351698115277034, 0.04852978149651612, 0.2563374460202912, 0.07868312568368593, 0.9507071563814276, 0.007940480658871889, 0.9455733391892027, 0.4761025393051341, 0.06329409664274364, 0.486108446887078, 0.6554607928409875, 0.3294403859657761, 0.02718898835050054, 0.2632599441236705, 0.09462189267290307, 0.2747185708643275, 0.01971954733787938, 0.9591589529807978, 0.445066915720239, 0.7380186230528726, 0.3686112558749921, 0.9765948224615983, 0.9830372572797934, 0.3428744949444181],\n+ [0.6626894690463668, 0.4168101145890417, 0.4227716136375318, 0.5460469376257381, 0.7920802349484392, 0.9148946082433389, 0.6025519507878634, 0.757695330723024'..b'+ "proportion":0\n+ },\n+ "2":{\n+ "omega":1.00002621592498,\n+ "proportion":0.6185938027364208\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":41\n+ },\n+ "RELAX null":{\n+ "AIC-c":6910.777215627525,\n+ "Log Likelihood":-3414.491942969586,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04600287725570656\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3432466763494891\n+ },\n+ "2":{\n+ "omega":1.896477292815783,\n+ "proportion":0.6107504463948045\n+ }\n+ },\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.2641095265325168,\n+ "rate":0.2744837794048847\n+ },\n+ "1":{\n+ "proportion":0.6330324513232739,\n+ "rate":0.9729462345446451\n+ },\n+ "2":{\n+ "proportion":0.1028580221442092,\n+ "rate":3.029415427453047\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04600287725570656\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3432466763494891\n+ },\n+ "2":{\n+ "omega":1.896477292815783,\n+ "proportion":0.6107504463948045\n+ }\n+ }\n+ },\n+ "display order":3,\n+ "estimated parameters":40\n+ },\n+ "RELAX partitioned descriptive":{\n+ "AIC-c":6909.42794543134,\n+ "Log Likelihood":-3408.579104294618,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0.05035684771569529,\n+ "proportion":0.3805224005150026\n+ },\n+ "1":{\n+ "omega":0.07013486723985318,\n+ "proportion":0.003462124163764896\n+ },\n+ "2":{\n+ "omega":2.344944921144001,\n+ "proportion":0.6160154753212325\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.03160127773820932\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.4079248249859382\n+ },\n+ "2":{\n+ "omega":1.11269394570475,\n+ "proportion":0.5604738972758525\n+ }\n+ }\n+ },\n+ "display order":5,\n+ "estimated parameters":45\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((PIG:0.147969,COW:0.21343)Node3:0.08509899999999999,HORSE:0.165787,CAT:0.264806)Node2:0.058611,((RHMONKEY:0.002015,BABOON:0.003108)Node9:0.022733,(HUMAN:0.004349,CHIMP:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,RAT:0.050958,MOUSE:0.09795)"\n+ }\n+ },\n+ "test results":{\n+ "LRT":11.47546300090198,\n+ "p-value":0.0007052107640865835,\n+ "relaxation or intensification parameter":2.986519568748539e-05\n+ },\n+ "tested":{\n+ "0":{\n+ "BABOON":"Test",\n+ "CAT":"Reference",\n+ "CHIMP":"Test",\n+ "COW":"Reference",\n+ "HORSE":"Reference",\n+ "HUMAN":"Test",\n+ "MOUSE":"Reference",\n+ "Node1":"Test",\n+ "Node12":"Test",\n+ "Node2":"Reference",\n+ "Node3":"Reference",\n+ "Node8":"Test",\n+ "Node9":"Test",\n+ "PIG":"Reference",\n+ "RAT":"Reference",\n+ "RHMONKEY":"Test"\n+ }\n+ },\n+ "timers":{\n+ "General descriptive model fitting":{\n+ "order":2,\n+ "timer":127\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":645\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":8\n+ },\n+ "RELAX alternative model fitting":{\n+ "order":3,\n+ "timer":178\n+ },\n+ "RELAX null model fitting":{\n+ "order":4,\n+ "timer":115\n+ },\n+ "RELAX partitioned descriptive":{\n+ "order":5,\n+ "timer":216\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 098451b762fb -r a4c5dc437558 test-data/relax-out2-2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out2-2.json Tue Apr 27 18:03:51 2021 +0000 |
| [ |
| b"@@ -0,0 +1,3427 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 10;\n+\tTAXLABELS\n+\t\t'HUMAN' 'CHIMP' 'BABOON' 'RHMONKEY' 'COW' 'PIG' 'HORSE' 'CAT' 'MOUSE' 'RAT' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 561;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'HUMAN' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'CHIMP' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'BABOON' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'RHMONKEY' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'COW' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT\n+\t'PIG' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT\n+\t'HORSE' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATAT"..b'023*t*relax._shared_srv.rv_gdd*relax.test.theta_CT*relax.test.omega3;\n+relax.test_Q_component_3[60][56]:=0.1659124550130927*t*relax._shared_srv.rv_gdd*relax.test.theta_GT*relax.test.omega3;\n+relax.test_Q_component_3[60][57]:=0.2714859010999351*t*relax._shared_srv.rv_gdd*relax.test.theta_AT*relax.test.omega3;\n+relax.test_Q_component_3[60][58]:=0.2217183243979596*t*relax._shared_srv.rv_gdd*relax.test.theta_CT;\n+relax.test_Q_component_3[60][59]:=0.2755785876068215*t*relax._shared_srv.rv_gdd*relax.test.theta_GT*relax.test.omega3;\n+\n+\n+relax.test_pi={\n+{0.04876086397632926} \n+{0.03982224127745371} \n+{0.0494959405650269} \n+{0.04152830682371345} \n+{0.01810345074594235} \n+{0.01478480742075003} \n+{0.01837636270304883} \n+{0.01541821854326533} \n+{0.01892910005547028} \n+{0.01545910240515689} \n+{0.01921445878706794} \n+{0.01612140169177368} \n+{0.02829747763884322} \n+{0.02311011106415996} \n+{0.02872406592369408} \n+{0.02410019507229243} \n+{0.01663805943190806} \n+{0.01358804506433061} \n+{0.01688888041768248} \n+{0.01417018446135155} \n+{0.006177213955434187} \n+{0.005044834822351987} \n+{0.006270336287397383} \n+{0.00526096577332031} \n+{0.006458939937330408} \n+{0.005274916061901906} \n+{0.006556309326397028} \n+{0.005500904159606446} \n+{0.009655594186286731} \n+{0.007885574003572761} \n+{0.009801153568494354} \n+{0.008223407979974132} \n+{0.03327785448210915} \n+{0.02717750758119989} \n+{0.03377952261833742} \n+{0.02834184710178207} \n+{0.01235507229404208} \n+{0.01009019590244688} \n+{0.01254132667213156} \n+{0.01052248035033209} \n+{0.01291855364640413} \n+{0.01055038238273567} \n+{0.01311330258173711} \n+{0.01100238215235291} \n+{0.01931219560697892} \n+{0.0157719705998612} \n+{0.01960332955558842} \n+{0.01644767379420349} \n+{0.01965132601881859} \n+{0.02049322866376102} \n+{0.008933621043463411} \n+{0.007295949736387736} \n+{0.009068296583349953} \n+{0.007608523013862737} \n+{0.007628698224327205} \n+{0.009481877006094248} \n+{0.00795552712159237} \n+{0.01396413011303752} \n+{0.01140428846505027} \n+{0.01417464125436193} \n+{0.01189287130232129} \n+};\n+Model relax.test=(\'Exp(relax.test_Q_component_1)*1*relax.test.bsrel_mixture_aux_0+Exp(relax.test_Q_component_2)*1*(1-relax.test.bsrel_mixture_aux_0)*relax.test.bsrel_mixture_aux_1+Exp(relax.test_Q_component_3)*1*(1-relax.test.bsrel_mixture_aux_0)*(1-relax.test.bsrel_mixture_aux_1)\',relax.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n+TRY_NUMERIC_SEQUENCE_MATCH=0;\n+ACCEPT_ROOTED_TREES=0;\n+Tree O_SJmzEX.tree_id_0=((((PIG{relax.reference},COW{relax.reference})Node3{relax.reference},HORSE{relax.reference},CAT{relax.reference})Node2{relax.reference},((RHMONKEY{relax.test},BABOON{relax.test})Node9{relax.test},(HUMAN{relax.test},CHIMP{relax.test})Node12{relax.test})Node8{relax.test})Node1{relax.test},RAT{relax.reference},MOUSE{relax.reference});\n+\n+O_SJmzEX.tree_id_0.PIG.t=0.4536172365685577;\n+O_SJmzEX.tree_id_0.COW.t=0.6103212983838633;\n+O_SJmzEX.tree_id_0.Node3.t=0.2484758643179366;\n+O_SJmzEX.tree_id_0.HORSE.t=0.4753747079725157;\n+O_SJmzEX.tree_id_0.CAT.t=0.6775352409130856;\n+O_SJmzEX.tree_id_0.Node2.t=0.1183276378467358;\n+O_SJmzEX.tree_id_0.RHMONKEY.t=0.01420592464486799;\n+O_SJmzEX.tree_id_0.BABOON.t=0.00485857082125907;\n+O_SJmzEX.tree_id_0.Node9.t=0.1015257435189256;\n+O_SJmzEX.tree_id_0.HUMAN.t=0;\n+O_SJmzEX.tree_id_0.CHIMP.t=0.006303088015069631;\n+O_SJmzEX.tree_id_0.Node12.t=0.05697754732758539;\n+O_SJmzEX.tree_id_0.Node8.t=0.4948729770972781;\n+O_SJmzEX.tree_id_0.Node1.t=1.445991686991002;\n+O_SJmzEX.tree_id_0.RAT.t=0.1315597576696033;\n+O_SJmzEX.tree_id_0.MOUSE.t=0.2736332745970835;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n+SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n+\n+DataSet relax.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n+DataSetFilter relax.filter.default = CreateFilter(relax.codon_data,3,"0-560","5,4,6,7,3,2,0,1,9,8","TAA,TAG,TGA");\n+ASSUME_REVERSIBLE_MODELS=1;\n+USE_LAST_RESULTS=0;\n+LikelihoodFunction O_SJmzEX.likelihoodFunction = (relax.filter.default,O_SJmzEX.tree_id_0);\n+\n+END;\n\\ No newline at end of file\n' |