| Previous changeset 16:a61b2b6c7089 (2021-04-20) Next changeset 18:966ba45cbd44 (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_prime.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 |
| b |
| diff -r a61b2b6c7089 -r 6d29207a32c5 hyphy_prime.xml --- a/hyphy_prime.xml Tue Apr 20 19:54:11 2021 +0000 +++ b/hyphy_prime.xml Tue Apr 27 18:04:23 2021 +0000 |
| [ |
| @@ -1,27 +1,22 @@ <?xml version="1.0"?> -<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy0" profile="19.09"> +<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy1" profile="19.09"> <description>Property Informed Models of Evolution</description> <macros> <import>macros.xml</import> - <token name="@OPERATION@">PRIME</token> - <token name="@operation@">prime</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @SYMLINK_FILES@ @HYPHYMPI@ prime --alignment ./$input_file - #if $input_nhx: - --tree ./input.nhx - #end if + @INPUT_TREE@ --code '$gencodeid' - --branches '$branches' + @branch_options@ --pvalue '$p_value' --properties '$prop_set' + --impute-states '$impute_states' --output '$prime_output' - > '$prime_log' - ; - @CATCH_ERROR@ + @ERRORS@ ]]></command> <inputs> <expand macro="inputs"/> @@ -32,9 +27,9 @@ <option value="LCAP">LCAP</option> </param> <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> + <param argument="--impute-states" type="boolean" truevalue="Yes" falsevalue="No" label="Use site-level model fits to impute likely character states for each sequence"/> </inputs> <outputs> - <data name="prime_log" format="txt"/> <data name="prime_output" format="hyphy_results.json" /> </outputs> <tests> |
| b |
| diff -r a61b2b6c7089 -r 6d29207a32c5 macros.xml --- a/macros.xml Tue Apr 20 19:54:11 2021 +0000 +++ b/macros.xml Tue Apr 27 18:04:23 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> |
| b |
| diff -r a61b2b6c7089 -r 6d29207a32c5 test-data/busted-in2.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-in2.nex Tue Apr 27 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 test-data/busted-out1.json --- a/test-data/busted-out1.json Tue Apr 20 19:54:11 2021 +0000 +++ b/test-data/busted-out1.json Tue Apr 27 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 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 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 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 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 test-data/gard-out1.json --- a/test-data/gard-out1.json Tue Apr 20 19:54:11 2021 +0000 +++ b/test-data/gard-out1.json Tue Apr 27 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 test-data/gard-out1.nex --- a/test-data/gard-out1.nex Tue Apr 20 19:54:11 2021 +0000 +++ b/test-data/gard-out1.nex Tue Apr 27 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 test-data/relax-in2.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nex Tue Apr 27 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 test-data/relax-out1.json --- a/test-data/relax-out1.json Tue Apr 20 19:54:11 2021 +0000 +++ b/test-data/relax-out1.json Tue Apr 27 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 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 18:04:23 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 a61b2b6c7089 -r 6d29207a32c5 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 18:04:23 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' |