| Next changeset 1:8f66e659530b (2020-04-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5" |
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added:
hyphy_prime.xml macros.xml test-data/absrel-in1.fa test-data/absrel-in1.nhx test-data/absrel-out1.json test-data/bgm-in1.fa test-data/bgm-in1.nhx test-data/bgm-out1.json test-data/busted-out1.json test-data/fade-in1.fa test-data/fade-in1.nhx test-data/fade-out1.json test-data/fel-out1.json test-data/fubar-in1.fa test-data/fubar-in1.nhx test-data/fubar-out1.json test-data/gard-in1.fa test-data/gard-out1.json test-data/gard-out1.nex test-data/meme-in1.fa test-data/meme-in1.nhx test-data/meme-out1.json test-data/params.json test-data/prime-in1.fa test-data/prime-in1.nhx test-data/prime-out1.json test-data/relax-in1.fa test-data/relax-in1.nhx test-data/relax-in2.nhx test-data/relax-out1.json test-data/slac-out1.json test-data/sm19-in1.nhx test-data/sm19-in2.nhx test-data/sm19-out1.json test-data/sm19-out2.json |
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| diff -r 000000000000 -r 725ef5f6d749 hyphy_prime.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_prime.xml Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| @@ -0,0 +1,132 @@ +<?xml version="1.0"?> +<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy0"> + <description>Property Informed Models of Evolution</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_file' prime_input.fa && + ln -s '$input_nhx' prime_input.nhx && + @HYPHYMPI@ prime + --alignment ./prime_input.fa + --tree ./prime_input.nhx + --code '$gencodeid' + --branches '$branches' + --pvalue '$p_value' + --properties '$prop_set' + --output '$prime_output' + > '$prime_log' + ; + @CATCH_MPIERR@ + ]]></command> + <inputs> + <expand macro="inputs"/> + <expand macro="gencode"/> + <expand macro="branches"/> + <param name="prop_set" type="select" label="Biochemical properties to use"> + <option value="Atchley">Atchley</option> + <option value="LCAP">LCAP</option> + </param> + <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> + </inputs> + <outputs> + <data name="prime_log" format="txt"/> + <data name="prime_output" format="hyphy_results.json" /> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fasta" value="prime-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="prime-in1.nhx"/> + <param name="branches" value="All"/> + <param name="p_value" value="0.1"/> + <param name="prop_set" value="Atchley"/> + <output name="prime_output" file="prime-out1.json" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +PRIME: Property Informed Model of Evolution +=========================================== + +What question does this method answer? +-------------------------------------- + +Does evolution at specific sites in a coding alignment preserve or alter some biochemical properties? + +Recommended Applications +------------------------ + +Identify biochemical evolutionary constraints or changes with site level resolution: e.g. site 23 is +evolving to conserve residue polarity, but alter it's volume. + + +Brief description +----------------- + +Most methods of coding sequence analysis do not take direct account of the fact that +the rate at which amino-acids are exchanged is different depending on the amino-acids. +While this seems obvious (e.g. radical changes should happen slower), there are many technical reasons +for why the standard assumption of "one-rate for all residues" holds. + + +Given a set of N amino-acid properties, fit a site-level model where non-synonymous rates +depend on how much a non-synonymous substitution changes the properties +of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- +lambda_2 * diff_2 (X,Y) -...). When lambda_k > 0, changes in property k +are disfavored and when lambda_k < 0 -- they are promoted. At each site, +N+1 tests are performed (one for each property, and an omnibus test). + +Input +----- + +1. A *FASTA* sequence alignment. +2. A phylogenetic tree in the *Newick* format + +Note: the names of sequences in the alignment must match the names of the sequences in the tree. + + +Output +------ + +A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). + +A custom visualization module for viewing these results will soon be available at http://vision.hyphy.org/ + +Further reading +--------------- + +http://hyphy.org/methods/selection-methods/#PRIME + + +Tool options +------------ +:: + + + --code Which genetic code to use + + --branches Which branches should be tested for selection? + All [default] : test all branches + + Internal : test only internal branches (suitable for + intra-host pathogen evolution for example, where terminal branches + may contain polymorphism data) + + Leaves: test only terminal (leaf) branches + + Unlabeled: if the Newick string is labeled using the {} notation, + test only branches without explicit labels + (see http://hyphy.org/tutorials/phylotree/) + + --pvalue The significance level used to determine significance + + --properties Which property set to use + Atchley : Use the five properties derived from a factor analysis of 500 amino-acid properties [Table 2 in PNAS (2005) 102(18) 6395-6400 doi: 10.1073/pnas.0408677102] + LCAP: Use the five properties defined in the Conant and Stadler LCAP model [Mol Biol Evol (2009) 26 (5): 1155-1161. doi: 10.1093/molbev/msp031] + + + ]]></help> + <!--<expand macro="citations"> + <citation type="doi">10.1371/journal.pgen.1002764</citation> + </expand>--> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 725ef5f6d749 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Mar 27 13:15:01 2020 -0400 |
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| @@ -0,0 +1,131 @@ +<?xml version="1.0"?> +<macros> + <xml name="inputs"> + <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> + <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> + </xml> + <xml name="substitution"> + <param name="model" type="select" label="Substitution model"> + <option value="GTR">GTR - General time reversible + model</option> + <option value="LG">LG - Generalist empirical model from + Le and Gascuel (2008)</option> + <option value="HIVBm">HIVBm - Specialist empirical model + for between-host HIV sequences</option> + <option value="HIVWm">HIVWm - Specialist empirical model + for within-host HIV sequences</option> + <option value="WAG">WAG - Generalist empirical model from + Whelan and Goldman (2001)</option> + <option value="JTT">JTT - Generalist empirical model from + Jones, Taylor, and Thornton (1996)</option> + <option value="JC69">JC69 - Generalist empirical model + from with equal exchangeability rates</option> + <option value="mtMet">mtMet - Specialist empirical model + for metazoan mitochondrial genomes</option> + <option value="mtVer">mtVer - Specialist empirical model + for vertebrate mitochondrial genomes</option> + <option value="mtInv">mtInv - Specialist empirical model + for invertebrate mitochondrial genomes</option> + <option value="gcpREV">gcpREV - Specialist empirical + model for green plant chloroplast genomes</option> + </param> + </xml> + + <xml name="conditional_posteriorEstimationMethod"> + <conditional name="posteriorEstimationMethod"> + <param argument="--method" type="select" label="Posterior estimation method"> + <option value="Variational-Bayes">0-th order Variational Bayes approximation</option> + <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option> + <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option> + </param> + <when value="Variational-Bayes"> + </when> + <when value="Metropolis-Hastings"> + <expand macro="mcmc_options" /> + </when> + <when value="Collapsed-Gibbs"> + <expand macro="mcmc_options" /> + </when> + </conditional> + </xml> + + <token name="@posteriorEstimationMethod_cmd@"> + #if $posteriorEstimationMethod.method != "Variational-Bayes" + --chains '$posteriorEstimationMethod.chains' + --chain-length '$posteriorEstimationMethod.chain_length' + --burn-in '$posteriorEstimationMethod.samples' + --samples '$posteriorEstimationMethod.samples_per_chain' + #end if + </token> + + <xml name="mcmc_options"> + <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" /> + <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" /> + <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" /> + <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" /> + </xml> + + <xml name="gencode"> + <param name="gencodeid" type="select" label="Genetic code"> + <option value="Universal">Universal code</option> + <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA + code</option> + <option value="Yeast-mtDNA">Yeast mitochondrial DNA + code</option> + <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and + Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="Invertebrate-mtDNA">Invertebrate mitochondrial + DNA code</option> + <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and + Hexamita Nuclear code</option> + <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA + code</option> + <option value="Euplotid-Nuclear">Euplotid Nuclear + code</option> + <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear + code</option> + <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA + code</option> + <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA + code</option> + <option value="Blepharisma-Nuclear">Blepharisma Nuclear + code</option> + </param> + </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> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/molbev/msz197</citation> + <yield/> + </citations> + </xml> + <token name="@VERSION@">2.5.8</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">hyphy</requirement> + <yield/> + </requirements> + </xml> + <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> + <token name="@CATCH_MPIERR@"><![CDATA[ + EC=\$? ; + if [ \$EC -ne 0 ] ; then + cat errors.log.mpinode0 >&2 ; + fi ; + exit \$EC + ]]></token> + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ + export HYPHY=`which hyphy` && + export HYPHY_PATH=`dirname \$HYPHY` && + export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> + <token name="@HYPHY_INVOCATION@"><![CDATA[ + @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB + ]]></token> +</macros> |
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| diff -r 000000000000 -r 725ef5f6d749 test-data/absrel-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
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| @@ -0,0 +1,20 @@ +>Human +AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Chimp +GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Baboon +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>RhMonkey +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Cow +------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT +>Pig +---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT +>Horse +------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT +>Cat +---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC +>Mouse +---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC +>Rat +---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC |
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| diff -r 000000000000 -r 725ef5f6d749 test-data/absrel-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
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| @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.097950); \ No newline at end of file |
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| diff -r 000000000000 -r 725ef5f6d749 test-data/absrel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-out1.json Fri Mar 27 13:15:01 2020 -0400 |
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| b'@@ -0,0 +1,456 @@\n+{\n+ "analysis":{\n+ "info":"aBSREL (Adaptive branch-site random effects likelihood)\\n uses an adaptive random effects branch-site model framework\\n to test whether each branch has evolved under positive selection,\\n using a procedure which infers an optimal number of rate categories per branch.",\n+ "version":"2.0",\n+ "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",\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"\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_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":-3531.96369518556,\n+ "estimated parameters":24,\n+ "AIC-c":7112.577796875186,\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":0.5474707834424497,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544\n+ },\n+ "display order":0\n+ },\n+ "Baseline MG94xREV":{\n+ "Log Likelihood":-3450.669934819203,\n+ "estimated parameters":46,\n+ "AIC-c":6995.711784065174,\n+ "Equilibrium frequencies":[\n+ [0.04787662253946073],\n+ [0.03913388100305117],\n+ [0.04844580322128512],\n+ [0.0407178971288476],\n+ [0.01817959331488358],\n+ [0.01485982100934833],\n+ [0.01839572120297191],\n+ [0.01546129971531724],\n+ [0.0190238172858878],\n+ [0.01554988139098808],\n+ [0.01924998172104109],\n+ [0.01617929156565557],\n+ [0.02798385246472159],\n+ [0.02287372613761008],\n+ [0.02831653817605838],\n+ [0.02379958245776909],\n+ [0.01680670574479072],\n+ [0.01373763619452979],\n+ [0.01700651207463693],\n+ [0.01429369239710176],\n+ [0.006381800954137531],\n+ [0.005216421415661322],\n+ [0.006457670922102578],\n+ [0.00542756570877943],\n+ [0.006678159032689796],\n+ [0.005458661598138652],\n+ [0.00675755225029668],\n+ [0.00567961101013393],\n+ [0.009823507779659469],\n+ [0.008029638769211124],\n+ [0.009940294440024354],\n+ [0.008354653231583485],\n+ [0.0329096029621651],\n+ [0.02689998621179963],\n+ [0.03330084840219455],\n+ [0.02798881284619018],\n+ [0.01249635346589736],\n+ [0.01021439657952951],\n+ [0.01264491622176376],\n+ [0.01062784315018763],\n+ [0.01307665913959002],\n+ [0.01068873273724336],\n+ [0.0132321208528494],\n+ [0.01112137894012831],\n+ [0.01923563996618058],\n+ [0.01572302316926395],\n+ [0.01946432265285621],\n+ [0.01635944157725275],\n+ [0.01977100255021048],\n+ [0.02057127040149398],\n+ [0.009184593415672956],\n+ 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"Full adaptive model":0.2165540926910564,\n+ "Rate Distributions":[\n+ [1, 0.9077840705139004],\n+ [33.32075865076668, 0.09221592948609958]\n+ ],\n+ "LRT":7.97288393366216,\n+ "Uncorrected P-value":0.006519360772582139,\n+ "Corrected P-value":0.08475169004356781\n+ },\n+ "Node9":{\n+ "Nucleotide GTR":0.02566719422260768,\n+ "Baseline MG94xREV":0.02590165433349057,\n+ "Baseline MG94xREV omega ratio":0.4071738826525522,\n+ "Rate classes":1,\n+ "Full adaptive model":0.02766629863085238,\n+ "Rate Distributions":[\n+ [0.4488424899910019, 1]\n+ ],\n+ "LRT":0,\n+ "Uncorrected P-value":1,\n+ "Corrected P-value":1\n+ }\n+ },\n+ "attributes":{\n+ "original name":{\n+ "attribute type":"node label",\n+ "display order":-1\n+ },\n+ "Nucleotide GTR":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ },\n+ "Baseline MG94xREV":{\n+ "attribute type":"branch length",\n+ "display order":1\n+ },\n+ "Baseline MG94xREV omega ratio":{\n+ "attribute type":"branch label",\n+ "display order":1\n+ },\n+ "Rate classes":{\n+ "attribute type":"branch label",\n+ "display order":2\n+ },\n+ "Full adaptive model":{\n+ "attribute type":"branch length",\n+ "display order":2\n+ },\n+ "Rate Distributions":{\n+ "attribute type":"branch label",\n+ "display order":3\n+ },\n+ "LRT":{\n+ "attribute type":"branch label",\n+ "display order":4\n+ },\n+ "Uncorrected P-value":{\n+ "attribute type":"branch label",\n+ "display order":5\n+ },\n+ "Corrected P-value":{\n+ "attribute type":"branch label",\n+ "display order":6\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/bgm-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>Human +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Chimp +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Baboon +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>RhMonkey +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>Cow +GCACGAATAAAGAAAGATATGCCACTTCAC +>Pig +GCAGAATTTAAAAAAAACAAAGAAACTCAC +>Horse +GCAAAATTCAAAAATGGCAGTATGACTTTC +>Cat +GCGAGGTTCCAAATTAGCAACAAGCCTAAG +>Mouse +GCAGAGTTTAAAAGGAAGAAGCCACCTTTT +>Rat +GCCGAGTTTAAAAGGAAGATGAAGCCTTTT |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/bgm-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.097950); |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/bgm-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| @@ -0,0 +1,168 @@ +{ + "MLE":{ + "content": [ +[2, 3, 0.02851572177464722, 0.01992394838090668, 0.04843967015555389, 4, 3, 1], + [2, 4, 0.2913031811286725, 0.1581095173619919, 0.4494126984906644, 4, 2, 2], + [2, 5, 0.04313828130286183, 0.09337388689236253, 0.1365121681952244, 4, 3, 2], + [2, 6, 0.05037434713194238, 0.07113225549859428, 0.1215066026305367, 4, 6, 3], + [2, 7, 0.2804886800096655, 0.2001828066808252, 0.4806714866904907, 4, 4, 3], + [2, 8, 0.07183821900324161, 0.1469389589305462, 0.2187771779337878, 4, 5, 3], + [2, 9, 0.03082407077478325, 0.09900473652454521, 0.1298288072993285, 4, 3, 2], + [2, 10, 0.02245776059232202, 0.02955557233236829, 0.05201333292469031, 4, 3, 1], + [3, 4, 0.03717045364745913, 0.02520976460488304, 0.06238021825234218, 3, 2, 0], + [3, 5, 0.02873335174526813, 0.03479214292405394, 0.06352549466932207, 3, 3, 1], + [3, 6, 0.1236923855363388, 0.2512471049857198, 0.3749394905220587, 3, 6, 3], + [3, 7, 0.01909635400892135, 0.02551889926711521, 0.04461525327603656, 3, 4, 1], + [3, 8, 0.02488014112561441, 0.05406148356625361, 0.07894162469186802, 3, 5, 2], + [3, 9, 0.08440837590482446, 0.2181470609147132, 0.3025554368195377, 3, 3, 2], + [3, 10, 0.1267967238159999, 0.1611592144212058, 0.2879559382372058, 3, 3, 2], + [4, 5, 0.03705892982325252, 0.07620033982326219, 0.1132592696465147, 2, 3, 1], + [4, 6, 0.01210885428759886, 0.04049276326654051, 0.05260161755413936, 2, 6, 1], + [4, 7, 0.03773982374178716, 0.04469577929352821, 0.08243560303531537, 2, 4, 1], + [4, 8, 0.02406357502679824, 0.04542327412998536, 0.06948684915678359, 2, 5, 1], + [4, 9, 0.04518375503528457, 0.08175199548949739, 0.126935750524782, 2, 3, 1], + [4, 10, 0.05271458150974553, 0.07030981080391227, 0.1230243923136578, 2, 3, 1], + [5, 6, 0.1359282078272841, 0.1540926795656895, 0.2900208873929736, 3, 6, 3], + [5, 7, 0.09099743539437326, 0.04199316180345154, 0.1329905971978248, 3, 4, 2], + [5, 8, 0.1895195673806065, 0.2930011407919719, 0.4825207081725784, 3, 5, 3], + [5, 9, 0.1148199627842869, 0.1105571269028783, 0.2253770896871652, 3, 3, 2], + [5, 10, 0.1270434887308012, 0.1100230063742557, 0.2370664951050569, 3, 3, 2], + [6, 7, 0.09069770755435493, 0.0484084497358865, 0.1391061572902414, 6, 4, 3], + [6, 8, 0.1325890592140632, 0.1385237411340729, 0.2711128003481361, 6, 5, 4], + [6, 9, 0.1237432424538594, 0.1610336810828299, 0.2847769235366894, 6, 3, 3], + [6, 10, 0.2074649804257667, 0.132053108013182, 0.3395180884389487, 6, 3, 3], + [7, 8, 0.0894441901425615, 0.1431622704391284, 0.2326064605816899, 4, 5, 3], + [7, 9, 0.06037024754303832, 0.114173814968622, 0.1745440625116604, 4, 3, 2], + [7, 10, 0.02455907863678367, 0.02700169365828593, 0.0515607722950696, 4, 3, 1], + [8, 9, 0.2356164682007381, 0.275411073609017, 0.5110275418097552, 5, 3, 3], + [8, 10, 0.05927356969559661, 0.02598780235339034, 0.08526137204898694, 5, 3, 2], + [9, 10, 0.1776480482199785, 0.09671451255218226, 0.2743625607721607, 3, 3, 2] + ], + "headers": [ +["Site 1", "Index of site 1"], + ["Site 2", "Index of site 2"], + ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"], + ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"], + ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"], + ["Site 1 subs", "Substitution counts inferred for Site 1"], + ["Site 2 subs", "Substitution counts inferred for Site 2"], + ["Shared subs", "Substitutions shared by both sites"] + ] + }, + "analysis":{ + "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond", + "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950", + "contact":"apoon42@uwo.ca", + "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data. Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"1.1" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Cat":{ + "models.codon.MG_REV.ModelDescription":0.8288168941011919 + }, + "Chimp":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Cow":{ + "models.codon.MG_REV.ModelDescription":0.8164924147537205 + }, + "Horse":{ + "models.codon.MG_REV.ModelDescription":0.2841592907567805 + }, + "Human":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Mouse":{ + "models.codon.MG_REV.ModelDescription":0.1035113121392619 + }, + "Node1":{ + "models.codon.MG_REV.ModelDescription":0.5236339695213962 + }, + "Node12":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node2":{ + "models.codon.MG_REV.ModelDescription":0.08766202644314423 + }, + "Node3":{ + "models.codon.MG_REV.ModelDescription":0.2629569437833751 + }, + "Node8":{ + "models.codon.MG_REV.ModelDescription":0.07018254851044582 + }, + "Node9":{ + "models.codon.MG_REV.ModelDescription":0.03334231749233734 + }, + "Pig":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Rat":{ + "models.codon.MG_REV.ModelDescription":0.1018034850081214 + }, + "RhMonkey":{ + "models.codon.MG_REV.ModelDescription":0 + } + }, + "attributes":{ + "models.codon.MG_REV.ModelDescription":{ + "attribute type":"branch length", + "display order":0 + } + } + }, + "data partitions":{ + "0":{ + "coverage": [ +[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] + ], + "name":"bgm.filter.default" + } + }, + "fits":{ + "models.codon.MG_REV.ModelDescription":{ + "AIC-c":508.3788244913426, + "Log Likelihood":-208.6011769515537, + "Rate Distributions":null, + "display order":0, + "estimated parameters":31 + } + }, + "input":{ + "datatype":"codon", + "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa", + "number of sequences":10, + "number of sites":10, + "trees":{ + "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)" + } + }, + "settings":{ + "burn-in":10000, + "data-type":"codon", + "max-parents":1, + "min-subs":1, + "samples":100, + "steps":100000, + "threshold":0.5 + }, + "tested":0, + "timers":{ + "Baseline fit":{ + "order":1, + "timer":3 + }, + "Network inference":{ + "order":2, + "timer":0 + }, + "Overall":{ + "order":0, + "timer":3 + } + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/busted-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,394 @@\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, 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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+ ],\n+ "optimized null": [\n+[1.118923161648219, 0.9980202548897937, 0.9997654691276022, 1.028326548692021, 0.7919741374095479, 0.6742163346738066, 0.9701775068012184, 1.781350909123149, 2.014615609490285, 0.9375026657270238, 0.6503469909372603, 1.467509823797021, 1.009616470968526, 1.168421464905222, 0.59'..b'371867],\n+ [0.01052856463184265],\n+ [0.01292858539344675],\n+ [0.0105618754683007],\n+ [0.0131180965046964],\n+ [0.01101098350431497],\n+ [0.0193250328267319],\n+ [0.01578738770911659],\n+ [0.0196083049972345],\n+ [0.01645869298147252],\n+ [0.01962343746171723],\n+ [0.02045785777700414],\n+ [0.008926115885166477],\n+ [0.007292098982657142],\n+ [0.009056957588961733],\n+ [0.007602170831388156],\n+ [0.007626222986467745],\n+ [0.009471947420992787],\n+ [0.007950502328516303],\n+ [0.01395367801862353],\n+ [0.01139931439306339],\n+ [0.01415821524731906],\n+ [0.01188403168729233] \n+ ],\n+ "Log Likelihood":-3467.004808147542,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.9950576192409499, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":31\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.85745601076,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.321297387654,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,\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+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ },\n+ "Unconstrained model":{\n+ "AIC-c":6910.766610587704,\n+ "Log Likelihood":-3414.486640449675,\n+ "Rate Distributions":{\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.2645541257391169,\n+ "rate":0.2747941124675511\n+ },\n+ "1":{\n+ "proportion":0.6325830460054784,\n+ "rate":0.9734675888351726\n+ },\n+ "2":{\n+ "proportion":0.1028628282554047,\n+ "rate":3.028333913894314\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04809457608200497\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3410012743721951\n+ },\n+ "2":{\n+ "omega":1.89363684081788,\n+ "proportion":0.6109041495458\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":40\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_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)Node3:0.08509899999999999,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":10.17362366082671,\n+ "p-value":0.003088842014430382\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":62\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":228\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":161\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fade-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,50 @@ +>Human +KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Chimp +EEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Baboon +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKIKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>RhMonkey +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIRWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKXKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTXPELNLYQDGKHVK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>Cow +----ESIVVWGALDHDLNLDIPGFPRSDIVADIKWNR--NKNKIARIKKDMPLHNEMDKY +DMFTNGTLKIKT-LMRNDSGLYEVEVYDSNGVNLLSKKFDLKIQEMLSGPEINWICTNRT +VSCKVENGSNPKLQLFLNTTRVKQDHGKLITYTWNTRWNKTFKCVASNHVDSKVSIEIAV +CPDEGLD +>Pig +-----TEVVWGIVDQDINLDIPELSKHDNVDHIRWQK--NENKIAEFKKNKETHPVKDTY +MMLPNGTLRIKD-LKRDDEGIYKVTVYATDGKHMLERKFDLPILDGVSKPVISWSCADKT +VTCEVAEGSDPKLKLYVNKSTAREGRQKVILWKWNTKWSTLFKCVASNNASEQISMVTIS +CTGQGLD +>Horse +----KNITILGALERDINLDIPAFQMSEHVEDIQWSK--GKTKIAKFKNGSMTFQKDKTY +EVLKNGTLKIKH-LERIHEGTYKVDAYDSDGKNVLEETFHLSLLEMVSKPNISWSCTNTT +LTCEVTKGTDFELKLYLNGRMIQKSPRKVIVYKRASNQIASFKCTANNTVSEESSSVVIR +CTEKGLD +>Cat +---ANDDIVWGTLGQDINLDIPDSQ-GINIDDIHWEK--GKKKVARFQISNKPKNPDEKY +NVSMNGTLKIKH-LMLEDCDTYKVVIYDKDGKNVLDKTFQLKIQEKVSTPNIDWNCINKT +LVCKVSNGTDPELKLYVNGTSIKPVSSKFSTYRFINKQKILVNCTAENKVSKESDVKMIT +CSEKGLD +>Mouse +---RDNETIWGVLGHGITLNIPNFQMTDDIDEVRWVR--RGTLVAEFKRKKPPFLISETY +EVLANGSLKIKKPMMRNDSGTYNVMVYGTNGMTRLEKDLDVRILERVSKPMIHWECPNTT +LTCAVLQGTDFELKLYQGETLLNSLPQKNMSYQW-TNLNAPFKCEAINPVSKESKMEVVN +CPEKGLS +>Rat +---RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWER--GSTLVAEFKRKMKPFLKSGAF +EILANGDLKIKN-LTRDDSGTYNVTVYSTNGTRILDKALDLRILEMVSKPMIYWECSNAT +LTCEVLEGTDVELKLYQGKEHLRSLRQKTMSYQW-TNLRAPFKCKAVNRVSQESEMEVVN +CPEKGLP |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fade-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958):0.1,Mouse:0.097950); |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fade-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,4281 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[11.51603702583788, 5.631258087856319, 0.9499945736517019, 1.039547845181838],\n+ [1.097681549705998, 5.630570600846716, 0.947706309872091, 0.9916649771782264],\n+ [1.539775545261955, 5.630630056322405, 0.9478739114757647, 0.9950294283968122],\n+ [1.667724788704626, 5.630719725601435, 0.9499994157127767, 1.039653814109997],\n+ [1.25847739711632, 5.630686152901463, 0.949999717667571, 1.039660423096818],\n+ [4.185910849001634, 5.630654866793391, 0.9499999990566257, 1.039666582026189],\n+ [17.36207569658563, 5.630654762177219, 0.9499999999975496, 1.039666602620866],\n+ [1.24218514731028, 5.630683377853925, 0.9499997426265079, 1.039660969385093],\n+ [1.024191826188649, 5.630715314989586, 0.9499994553820734, 1.039654682360772],\n+ [1.014004796667106, 5.632607163746273, 0.9499824399855789, 1.039282388967598],\n+ [0.4740621651395832, 5.627503581943447, 0.9444437370511891, 0.9302154716674949],\n+ [0.9140592541745473, 5.630730160151203, 0.9499993218638363, 1.039651760022723],\n+ [0.7567550781917379, 5.633990183409649, 0.949970001027206, 1.039010387334885],\n+ [0.9228460004688066, 5.631089594644688, 0.9499960890893352, 1.039581008459963],\n+ [0.7121146981259312, 5.630928767310179, 0.9499975355796291, 1.03961266479502],\n+ [0.6095796503565455, 5.637045393913153, 0.9499425222882696, 1.038409991274629],\n+ [0.6605558065143393, 5.63554887505476, 0.9499559820649285, 1.0387039979643],\n+ [0.7334618546894945, 5.631584447719907, 0.9499916383523238, 1.039483615889978],\n+ [0.504224974984698, 5.628287880610704, 0.945085891537364, 0.9417330997713343],\n+ [0.5854212568599715, 5.637914315759457, 0.949934707155223, 1.038239355084906],\n+ [0.4134221795168672, 5.624771969338814, 0.9425950877828698, 0.8984969502868022],\n+ [0.3904522005816345, 5.623504918093849, 0.9417960395092443, 0.8854107996422699],\n+ [2.212335991763995, 5.630654963724663, 0.9499999981848204, 1.039666562944362],\n+ [0.9394451709609548, 5.631043490270708, 0.9499965037547257, 1.039590083194665],\n+ [0.662131332286878, 5.63206552947176, 0.9499873114753865, 1.039388950286528],\n+ [0.6265288978761459, 5.632604714967718, 0.9499824620100337, 1.039282870694441],\n+ [0.8073383340999795, 5.630800914362855, 0.9499986854963882, 1.039637831946584],\n+ [0.7792544736123335, 5.63140929379169, 0.9499932136968249, 1.039518086142237],\n+ [1.454921870901184, 5.630658037203366, 0.9499999705417759, 1.039665957901579],\n+ [0.8187160463016893, 5.631238578773209, 0.949994749117517, 1.039551684908112],\n+ [0.7579513217946872, 5.631482189124849, 0.9499925580720074, 1.039503740093819],\n+ [0.7197156570640451, 5.631648897767064, 0.9499910586848941, 1.039470932682291],\n+ [0.6214790654256428, 5.636571110701319, 0.9499467880187472, 1.038503152027503],\n+ [1.057135219780293, 5.630660196325318, 0.9499999511225089, 1.039665532858806],\n+ [0.6108370616594117, 5.629852062445075, 0.9466008848231501, 0.9700035810798537],\n+ [1.302972523179607, 5.630665076132612, 0.9499999072332416, 1.039664572225623],\n+ [0.6199990540154902, 5.632759480958808, 0.9499810700358113, 1.039252425764596],\n+ [1.201664187292616, 5.630591693857761, 0.9477598036683865, 0.992736471372866],\n+ [1.125320876061587, 5.630581829699935, 0.947731859108226, 0.9921764611988656],\n+ [1.663131794636887, 5.630679928739902, 0.9499997736480377, 1.039661648369019],\n+ [1.373376890533494, 5.630675820666751, 0.949999810596284, 1.039662457075089],\n+ [1.009621807867757, 5.630729047751628, 0.9499993318688219, 1.03965197900313],\n+ [0.7922677004712597, 5.631579600918412, 0.9499916819447352, 1.039484569710167],\n+ [0.8020493394401262, 5.631282254381984, 0.9499943562965806, 1.039543088827367],\n+ [0.3617783815235022, 5.6211737'..b'T7", "T->E(1)K(1)R(1)S(1)"],\n+ ["H11,L1,M1,R2,S1,T1", "H->L(1)M(1)R(1)S(1), R->T(1)"],\n+ ["A1,I4,L10,V2", "I->A(1)V(1), L->I(1)V(1)"],\n+ ["K12,N1,Q1,R3", "K->Q(1)R(1), R->K(1)N(1)"],\n+ ["E4,K1,P1,Q1,S3", "E->K(1)P(1)Q(1), S->E(1)"],\n+ ["D1,G2,L12,S1,V1", "G->D(1), L->G(1)S(1)V(1)"],\n+ ["H1,P3,R2,S11", "P->R(1)S(1), S->H(1)P(1)R(1)"],\n+ ["G1,Q14,R1,S1", "Q->G(1)R(1)S(1)"],\n+ ["K10,R7", "K->R(1)"],\n+ ["F1,L1,N1,T2,V12", "T->N(1)V(1), V->F(1)L(1)"],\n+ ["I13,M3,S1", "I->S(1), M->I(1)"],\n+ ["L1,S3,T12,V1", "S->T(1), T->L(1)V(1)"],\n+ ["H7,W1,Y9", "Y->H(1)W(1)"],\n+ ["K12,Q3,R1,T1", "K->R(1)T(1), Q->K(1)"],\n+ ["F1,R1,W15", "W->F(1)R(1)"],\n+ ["A4,I1,N3,T7", "A->I(1)N(1)T(1)"],\n+ ["N1,S1,T15", "T->N(1)S(1)"],\n+ ["K3,N6,R1,S7", "K->R(1), N->K(2)S(1)"],\n+ ["L11,Q3,W3", "L->Q(1), Q->W(1)"],\n+ ["I1,K1,N2,R2,S11", "R->N(1)S(1), S->I(1)K(1)N(1)"],\n+ ["A13,I1,K1,T2", "A->I(1)T(1), T->K(1)"],\n+ ["K7,L2,P3,S1,T4", "P->T(1), T->K(1)L(2)S(1)"],\n+ ["F16,V1", "F->V(1)"],\n+ ["K16,N1", "K->N(1)"],\n+ ["C17", ""],\n+ ["E1,K2,T11,V3", "K->E(1)T(1), T->V(1)"],\n+ ["A17", ""],\n+ ["E1,G7,I2,N1,S5,V1", "I->S(1)V(1), S->E(1)G(1)N(1)"],\n+ ["N17", ""],\n+ ["H1,K10,N2,P1,R2,T1", "K->N(1)T(1), N->H(1), R->K(1)P(1)"],\n+ ["A1,V16", "V->A(1)"],\n+ ["D1,S16", "S->D(1)"],\n+ ["E3,K12,Q1,S1", "E->S(1), K->E(2)Q(1)"],\n+ ["E15,K1,Q1", "E->K(1)Q(1)"],\n+ ["I2,S14,V1", "I->V(1), S->I(1)"],\n+ ["D1,E2,K1,R3,S10", "E->K(1)S(1), S->D(1)R(1)"],\n+ ["I1,M11,S1,V4", "M->I(1)S(1)V(2)"],\n+ ["E14,K1,V2", "E->K(1)V(2)"],\n+ ["I1,M1,P3,T5,V7", "T->P(1), V->I(1)M(1)T(2)"],\n+ ["A1,I5,V11", "I->A(1), V->I(1)"],\n+ ["N3,R1,S11,T1,V1", "N->S(1), S->R(1)T(1)V(1)"],\n+ ["C17", ""],\n+ ["P14,S1,T2", "P->S(1)T(2)"],\n+ ["D1,E15,G1", "E->D(1)G(1)"],\n+ ["E1,K15,Q1", "K->E(1)Q(1)"],\n+ ["G17", ""],\n+ ["L17", ""],\n+ ["D14,P1,S2", "S->D(1)P(1)"] \n+ ]\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node10":"test",\n+ "Node13":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node4":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Baseline Fit":{\n+ "order":1,\n+ "timer":88\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":121\n+ },\n+ "Residue A analysis":{\n+ "order":2,\n+ "timer":2\n+ },\n+ "Residue C analysis":{\n+ "order":3,\n+ "timer":1\n+ },\n+ "Residue D analysis":{\n+ "order":4,\n+ "timer":1\n+ },\n+ "Residue E analysis":{\n+ "order":5,\n+ "timer":1\n+ },\n+ "Residue F analysis":{\n+ "order":6,\n+ "timer":2\n+ },\n+ "Residue G analysis":{\n+ "order":7,\n+ "timer":1\n+ },\n+ "Residue H analysis":{\n+ "order":8,\n+ "timer":2\n+ },\n+ "Residue I analysis":{\n+ "order":9,\n+ "timer":1\n+ },\n+ "Residue K analysis":{\n+ "order":10,\n+ "timer":2\n+ },\n+ "Residue L analysis":{\n+ "order":11,\n+ "timer":1\n+ },\n+ "Residue M analysis":{\n+ "order":12,\n+ "timer":2\n+ },\n+ "Residue N analysis":{\n+ "order":13,\n+ "timer":2\n+ },\n+ "Residue P analysis":{\n+ "order":14,\n+ "timer":1\n+ },\n+ "Residue Q analysis":{\n+ "order":15,\n+ "timer":2\n+ },\n+ "Residue R analysis":{\n+ "order":16,\n+ "timer":2\n+ },\n+ "Residue S analysis":{\n+ "order":17,\n+ "timer":2\n+ },\n+ "Residue T analysis":{\n+ "order":18,\n+ "timer":2\n+ },\n+ "Residue V analysis":{\n+ "order":19,\n+ "timer":2\n+ },\n+ "Residue W analysis":{\n+ "order":20,\n+ "timer":2\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":2\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fel-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,450 @@\n+{\n+ "analysis":{\n+ "info":"FEL (Fixed Effects Likelihood)\\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\\n The estimates aggregate information over all branches,\\n so the signal is derived from\\n pervasive diversification or conservation. A subset of branches can be selected\\n for testing as well, in which case an additional (nuisance) parameter will be\\n inferred -- the non-synonymous rate on branches NOT selected for testing.\\n Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n+ "version":"2.00",\n+ "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",\n+ "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "input":{\n+ "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.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)Node3:0.085099,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":-3531.963798530155,\n+ "estimated parameters":24,\n+ "AIC-c":7112.142458295762,\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":0.5474490057204714,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378\n+ },\n+ "display order":0\n+ },\n+ "Global MG94xREV":{\n+ "Log Likelihood":-3466.725508616141,\n+ "estimated parameters":31,\n+ "AIC-c":6996.530451399855,\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+ ['..b'871235417342727, 1.658943187728135],\n+ [0, 1.009408180447169, 0.7201317416266795, 1.906505699392216, 0.1673519284290025, 1.293896776352589],\n+ [1.701545575395463e-14, 1.16201561388296, 1.114130105107937, 0.2442491813364853, 0.6211538364843379, 1.489514634415266],\n+ [0.8883515458297054, 1.623622648529189, 1.334319744829745, 0.1803627821799836, 0.6710616565201941, 2.477143670911062],\n+ [0, 0.5570419450087813, 0.3610157342941877, 1.689213063741757, 0.193704737236408, 0.7140369881099469],\n+ [2.804120856177222e-15, 1.378683497609396, 1.139416739891161, 1.532228496397977, 0.215778295124767, 1.767247549328411],\n+ [0.630106498235145, 1.530183136222741, 1.176306017317766, 0.5627230344194487, 0.4531651666494674, 2.242273764894695],\n+ [4.996412325715582, 2.072849087019975, 2.501919619833955, 0.4374688424558926, 0.5083466741660978, 4.883875616363817],\n+ [1.476720795366284, 1.192713829097381, 1.265398043718104, 0.04756528081958322, 0.827355357807033, 2.187015539850353],\n+ [1.778599502537943, 2.833030015698272, 2.535624910277768, 0.2150914997093523, 0.642805674139892, 4.424176058896644],\n+ [1.502754420888704, 0.2825342556426603, 0.4733601919284142, 1.180637234982843, 0.2772263054246996, 1.031916435368656],\n+ [0, 0.2915937523113351, 0.2283654592452333, 0.4790160930559324, 0.4888683243803773, 0.3737756671964466],\n+ [10.08767614696688, 0, 0.4133910037948654, 8.462162631979279, 0.003626104567950983, 4.495915621518065],\n+ [1.984506219150062, 1.662771746660892, 1.756718773063347, 0.03121207319557584, 0.8597680862487451, 3.015865008244778],\n+ [3.805655301370652, 0, 0.7005303037771143, 11.62838958327228, 0.0006495276635800629, 1.696119588919385],\n+ [3.173406516538895, 2.860065663238961, 2.926441853316894, 0.003891888657044262, 0.9502562372040178, 5.080474489659786],\n+ [0, 0, 0, 0, 1, 0],\n+ [2.194271257132928, 4.019627316522699, 3.237226152191341, 0.09176983643381931, 0.7619391181878015, 6.130458650322728],\n+ [0, 0.2994174888128062, 0.1834705090468997, 0.9675444779876443, 0.3252933434590788, 0.3838044222970849],\n+ [1.737488918246139, 0.4263169813102716, 0.5705211950188817, 0.9504457433159637, 0.3296058631975952, 1.320839860569391],\n+ [9.491047642026737e-16, 2.201411562959478, 1.602398780540194, 2.916382754860905, 0.08768422447478674, 2.82185084281439],\n+ [1.033236674389839, 0.5673779129005597, 0.6682462878144323, 0.1916420169326862, 0.6615534805841186, 1.187783044398971],\n+ [0.6633763440867723, 2.065196310532788, 1.40713862608088, 0.9931353495817845, 0.318977273245592, 2.942901296371888],\n+ [3.88753619664278e-15, 1.779262169776622, 1.549159808629328, 1.288480285336618, 0.2563282037478503, 2.280724121673174],\n+ [137.6200023666397, 1.712312972734741, 2.612335663828599, 4.571254357285468, 0.03251275075427451, 63.52993609974021],\n+ [0.9069803858948896, 1.008331374883533, 0.9795641413367016, 0.006632998551161506, 0.9350894763840309, 1.696743112350582],\n+ [1.250218074119796, 2.685270528336648, 2.279331033581541, 0.4656302199387952, 0.4950043706394306, 3.99928134132692],\n+ [0.5981237480607854, 1.191515517605649, 0.9684057167421628, 0.3651500230254783, 0.5456598635374844, 1.793902873797072],\n+ [5.567356236371868, 1.655977785625157, 2.134648959148231, 0.8514639837247273, 0.3561385136046764, 4.60397510129604],\n+ [0, 0, 0, 0, 1, 0],\n+ [0.5915176036957202, 0.7772525687759813, 0.7215979531128016, 0.05398776775817282, 0.8162640993312603, 1.259941036310695],\n+ [0, 0.543676760549953, 0.4362855008937696, 0.8539326132569869, 0.3554421959431151, 0.6969049998601837],\n+ [1.00226665989553, 0.6268338660673796, 0.7169253651929272, 0.1172739583266811, 0.7320101172431673, 1.250193047146509],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [2.797676857161142, 0.824684447244541, 1.167394064072366, 1.285234262338761, 0.2569280765461694, 2.303990803636788]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fubar-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,326 @@\n+>KF789585\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCCCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGACACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAATTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n+>CY025485\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCATCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAGTGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGGAATCTGCAACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAATTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTGCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAGAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCAGCCTATATGCTCAAGCACCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCCGAGTAAGGGATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGACAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGCTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGACCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGACCTAACTGACTCAGAAATGAACAAATTGTTTGAAAGAACAAAAAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n+>KC535396\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGA'..b'GAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n+>CY012232\n+ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACAGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGATCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAGAGTTCCCCAACAGGTAGAATATGCGACAGTCCTCACCGAATCCTTGATGGAAAGAACTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAATAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACCCTGGAGTTTACCAACGAAAACTTCAATTGGACTGGAGTCGCTCAGGATGGGAAAAGCTATGCTTGCAAAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGCACAAATTAGAATACAAATATCCAGCGCTGAACGTGACTATGCCAAACAATGGCAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGAGCACGGACAGTGACCAAACCAGCCTATATGTCCGAGCATCAGGGAAAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGGATATCGGGTATAGACCATGGGTAAGGGGTCTTTCCAGTAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAATAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAATGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAACTGCAGTTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGCCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAGAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGACAAGCTGCAGATCTTAAAAGCACTCAAGCAGCAATCGACCAAATCAACGGGAAACTGAATAGGTTAGTCGAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAAGACACTAAAATAGATCTCTGGTCTTACAATGCGGAGCTTCTTGTTGCTCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTATTTGAAAGAACAAGGAAGCAACTGAGGGAAAATGCTGAGGACATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTTTGCTTGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n+>EU199367\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAGTCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fubar-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0; |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/fubar-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
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"Node84":"test",\n+ "Node85":"test",\n+ "Node86":"test",\n+ "Node90":"test",\n+ "Node91":"test",\n+ "Node93":"test",\n+ "Node96":"test",\n+ "Node97":"test",\n+ "Node99":"test"\n+ }\n+ },\n+ "timers":{\n+ "Grid Calculations":{\n+ "order":2,\n+ "timer":81\n+ },\n+ "Nucleotide Fit":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":87\n+ },\n+ "Posterior estimation":{\n+ "order":3,\n+ "timer":1\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/gard-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,120 @@ +>BRO1_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO2 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACCCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTGCATAAAGCCATTTACCGTACATA +GCACATTATA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO3_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAGCTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO4 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO5 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO6 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO7_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO8 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO9 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO10 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO11_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +TACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCC +CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO12 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC +TACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTC +CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC \ No newline at end of file |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/gard-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,318 @@\n+{\n+ "analysis":{\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+ "requirements":"A sequence alignment.",\n+ "version":"0.1"\n+ },\n+ "baselineScore":8884.998566352424,\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,(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+ "bps": [\n+[651, 1166] \n+ ],\n+ "tree":"(((((((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.'..b'((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+ "newickString":"((((((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,(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+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/meme-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,1 @@\n+>CHICKEN_HEBEI_326_2005\rATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAG\rAAGACACACAACGGGAAGCTCTGCAACCCAGATGGAGTGAAGCCTCTAAT\rTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTTATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGGCCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGGAGCCTCATCAGGGGTGAGCTCAGCA\rTGTTCCTATCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAATAATACATACCCACCAATAAAGGTGAGCTACAACAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCCAATGATGAG\rGCAGAGCAGATAAAGATCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\rCCGAATGATGCTATCAATTTCGATAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCGATTATGAAAAGTG\rAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCGTCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTCGCGACTGGACTCA\rGAAATGCCCCTCAAAGAGAGGGAGGAAGAAAAAAGAGAGGACTATTTGGA\rGCCATAGCAGGGTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAACGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCATTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r>MALLARD_VIETNAM_16_2003\rATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT\rCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGAATATGAAGAATT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGCA\rTGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTGT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGG\rGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAATATACACCCCCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA\rGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAAGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rCAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\rCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA---\r>CHICKEN_CK_160_2005\rATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGTGATCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTTGGAAACCCAATGTGTG\rATGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGT'..b'GGGAATTTAA\rCAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGGAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\rCAATTTATTCTACAGTAGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCCTTATGGATGTGCTTCAATGGGTCGTTACAATGCAGAATT\r>CK_HK_WF157_2003\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACCCACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTG\rACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCATCCAATGACCTCTGTTACCCAGGGGATTTCAACAATTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGCTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCCTTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGACTAGTCCTTGCGACTGGGCTCA\rGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCGGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTAGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACTCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGT------\r>SWINE_ANHUI_1_2004\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA\rTCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCACCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rGACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAAAGTG\rAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCG\rATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA\rGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAGATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCGGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTGGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/meme-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516):0.002095219592954275):0.003887237703073042)):0.003130608143291779,(CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849) |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/meme-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,2535 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 0, 3.477431520841965, 1, 0, 0.6666666666666666, 0, 0.1244820193331403],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 0, 3.741010141509965, 1, 0, 0.6666666666666666, 0, 0.1339173737771157],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 0, 3.515256679835982, 1, 0, 0.6666666666666666, 0, 0.1258360509351867],\n+ [0, 0, 0, 2.551430028273134, 1, 0, 0.6666666666666666, 0, 0.09133383654087057],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 0.09433309141367374, 3.23711069521408, 0.9056669085863263, 0.5595133528189606, 0.4135250593893275, 0, 0.1049479822225346],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 0, 4.065768798286446, 1, 0, 0.6666666666666666, 0, 0.1455427970670232],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [6.565759874687353, 0, 0.10495989356895, 0, 0.89504010643105, 0, 0.6666666666666666, 0, 0.1032447536564542],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [10.49514785248221, 0, 1.14531252379555e-10, 0, 0.9999999998854687, 0, 0.6666666666666666, 0, 0.1650332901748387],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [13.09135310777685, 0, 5.726562618977749e-11, 0, 0.9999999999427344, 0, 0.6666666666666666, 0, 0.2058578980100819],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [12.37490343362032, 0, 0.05858880329925001, 0, 0.94141119670075, 0, 0.6666666666666666, 0, 0.1945919255213972],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [987.5019115722299, 0, 0.0004, 0, 0.9996, 0, 0.6666666666666666, 0, 15.52819377215],\n+ [14.55761344047962, 3.151090015539141, 0, 3.15098583171967, 1, 0, 0.6666666666666666, 0, 0.3417106414963155],\n+ [0, 0, 0, 5.632316287317649, 1, 0, 0.6666666666666666, 0, 0.2016206791610606],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [5.480073695171225, 0, 5.529684747073369e-10, 0, 0.9999999994470316, 0, 0.6666666666666666, 0, 0.08617263949271516],\n+ [0, 0, 0, 2.821925207775446, 1, 0, 0.6666666666666666, 0, 0.1010167838433599],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [7.490255319000378, 0, 2.281746655933769e-10, 0, 0.9999999997718253, 0, 0.6666666666666666, 0, 0.1177821881996506],\n+ [17.81018664392365, 0, 0'..b'.01220539771302355],\n+ [0.01297489997065711],\n+ [0.01419701929364967],\n+ [0.02306796533539959],\n+ [0.0138011088931582],\n+ [0.01467121445635504],\n+ [0.01605311140503505],\n+ [0.03067687144383888],\n+ [0.01835336741416609],\n+ [0.01951047494908151],\n+ [0.02134818687672324],\n+ [0.02126077850204813],\n+ [0.01271990463804815],\n+ [0.01352184453103644],\n+ [0.01479548113102975],\n+ [0.008898103672735205],\n+ [0.005323560008197935],\n+ [0.005659189501089015],\n+ [0.006192234446128948],\n+ [0.010061425331433],\n+ [0.006019552422614294],\n+ [0.006399061496227086],\n+ [0.007001795754005012],\n+ [0.01338015932252603],\n+ [0.008005085543223482],\n+ [0.008509774660521757],\n+ [0.009311319186526256],\n+ [0.04013232935583105],\n+ [0.02401038147590574],\n+ [0.02552414146855538],\n+ [0.02792828690027832],\n+ [0.01679626299677307],\n+ [0.01004887302569606],\n+ [0.0106824148947738],\n+ [0.01168860266413242],\n+ [0.01899217543474583],\n+ [0.01136264414662781],\n+ [0.01207901411089265],\n+ [0.0132167490129733],\n+ [0.02525669324448205],\n+ [0.01511058165209229],\n+ [0.0160632443156804],\n+ [0.01757625800461362],\n+ [0.02112670632168297],\n+ [0.02457406668036405],\n+ [0.01477901198657192],\n+ [0.008841991514828857],\n+ [0.009399444257673735],\n+ [0.01028478768834936],\n+ [0.009997977173519282],\n+ [0.01062831025955897],\n+ [0.01162940185705429],\n+ [0.02222333457585675],\n+ [0.01329578296096281],\n+ [0.01413402971424556],\n+ [0.01546532867335853] \n+ ],\n+ "Log Likelihood":-2978.298667783946,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.2932353608697501, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":27\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":6152.529196194525,\n+ "Equilibrium frequencies": [\n+[0.3478363400542389],\n+ [0.184883858035609],\n+ [0.2307510906732697],\n+ [0.2365287112368824] \n+ ],\n+ "Log Likelihood":-3056.215005465311,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.1810796022573985,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.08708610799393901,\n+ "Substitution rate from nucleotide C to nucleotide G":0.02931879134098465,\n+ "Substitution rate from nucleotide C to nucleotide T":1.419136867291551,\n+ "Substitution rate from nucleotide G to nucleotide T":0.1065442350926398\n+ },\n+ "display order":0,\n+ "estimated parameters":20\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpdqyv1aux/job_working_directory/000/3/working/./meme_input.fa",\n+ "number of sequences":5,\n+ "number of sites":566,\n+ "partition count":1,\n+ "trees":{\n+ "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:-1)Node3:0.003130608143291779,(CK_HK_WF157_2003:0.00663129750258774)Node9:0.004655295319725731)Node2:0.0116808817874948,(MALLARD_VIETNAM_16_2003:0.003244216605281072)Node11:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "CHICKEN_CK_160_2005":"test",\n+ "CHICKEN_HEBEI_326_2005":"test",\n+ "CK_HK_WF157_2003":"test",\n+ "MALLARD_VIETNAM_16_2003":"test",\n+ "Node11":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node4":"test",\n+ "Node5":"test",\n+ "Node7":"test",\n+ "Node9":"test",\n+ "SWINE_ANHUI_1_2004":"test"\n+ }\n+ },\n+ "timers":{\n+ "MEME analysis":{\n+ "order":2,\n+ "timer":437\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":4\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":442\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/params.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/params.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,280 @@\n+{\n+ "filepath": "/home/sweaver/datamonkey/datamonkey-js-dev/app/models/../../uploads/msa/5446bc0d355080301f18a8c6.fasta",\n+ "msa": [\n+ {\n+ "rawsites": 1698,\n+ "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",\n+ "goodtree": 0,\n+ "sequences": 21,\n+ "sites": 566,\n+ "partitions": 1,\n+ "analysis_type": "1",\n+ "gencodeid": 0,\n+ "datatype": 0,\n+ "_id": "5446bc0d355080301f18a8c7",\n+ "created": "2014-10-21T20:03:25.803Z",\n+ "sequence_info": [\n+ {\n+ "seqindex": 0,\n+ "name": "TREESPARROW_HENAN_1_2004",\n+ "_id": "5446bc0d355080301f18a8c8"\n+ },\n+ {\n+ "seqindex": 1,\n+ "name": "HUMAN_VIETNAM_CL105_2005",\n+ "_id": "5446bc0d355080301f18a8c9"\n+ },\n+ {\n+ "seqindex": 2,\n+ "name": "TREESPARROW_HENAN_4_2004",\n+ "_id": "5446bc0d355080301f18a8ca"\n+ },\n+ {\n+ "seqindex": 3,\n+ "name": "CHICKEN_HEBEI_326_2005",\n+ "_id": "5446bc0d355080301f18a8cb"\n+ },\n+ {\n+ "seqindex": 4,\n+ "name": "CHICKEN_HONGKONG_915_97",\n+ "_id": "5446bc0d355080301f18a8cc"\n+ },\n+ {\n+ "seqindex": 5,\n+ "name": "HUMAN_VIETNAM_3062_2004",\n+ "_id": "5446bc0d355080301f18a8cd"\n+ },\n+ {\n+ "seqindex": 6,\n+ "name": "GOOSE_HONGKONG_W355_97",\n+ "_id": "5446bc0d355080301f18a8ce"\n+ },\n+ {\n+ "seqindex": 7,\n+ "name": "DUCK_HONGKONG_Y283_97",\n+ "_id": "5446bc0d355080301f18a8cf"\n+ },\n+ {\n+ "seqindex": 8,\n+ "name": "DUCK_VIETNAM_376_2005",\n+ "_id": "5446bc0d355080301f18a8d0"\n+ },\n+ {\n+ "seqindex": 9,\n+ "name": "MALLARD_VIETNAM_16_2003",\n+ "_id": "5446bc0d355080301f18a8d1"\n+ },\n+ {\n+ "seqindex": 10,\n+ "name": "CHICKEN_CK_160_2005",\n+ "_id": "5446bc0d355080301f18a8d2"\n+ },\n+ {\n+ "seqindex": 11,\n+ '..b'ex": 10\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d3",\n+ "name": "DUCK_GUANGZHOU_20_2005",\n+ "seqindex": 11\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d4",\n+ "name": "CK_HK_WF157_2003",\n+ "seqindex": 12\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d5",\n+ "name": "SWINE_ANHUI_1_2004",\n+ "seqindex": 13\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d6",\n+ "name": "DUCK_VIETNAM_272_2005",\n+ "seqindex": 14\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d7",\n+ "name": "HONGKONG_1_97_98",\n+ "seqindex": 15\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d8",\n+ "name": "GOOSE_SHANTOU_2216_2005",\n+ "seqindex": 16\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d9",\n+ "name": "TREESPARROW_HENAN_3_2004",\n+ "seqindex": 17\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8da",\n+ "name": "PEREGRINEFALCON_HK_D0028_2004",\n+ "seqindex": 18\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8db",\n+ "name": "TREESPARROW_HENAN_2_2004",\n+ "seqindex": 19\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8dc",\n+ "name": "HONGKONG_1_538_97",\n+ "seqindex": 20\n+ }\n+ ],\n+ "created": "2014-10-21T20:03:25.803Z",\n+ "_id": "5446bc0d355080301f18a8c7",\n+ "datatype": 0,\n+ "gencodeid": 0,\n+ "partitions": 1,\n+ "sites": 566,\n+ "sequences": 21,\n+ "goodtree": 0,\n+ "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",\n+ "rawsites": 1698\n+ }\n+ ],\n+ "created": "2014-10-21T20:03:25.798Z"\n+ },\n+ "status_stack": [\n+ "In Queue",\n+ "Running",\n+ "Completed"\n+ ],\n+ "type": "relax"\n+}\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/prime-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +>HUMAN_VIETNAM_CL105_2005 ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_HEBEI_326_2005 ATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAG >CHICKEN_HONGKONG_915_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HUMAN_VIETNAM_3062_2004 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_HONGKONG_W355_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >MALLARD_VIETNAM_16_2003 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_CK_160_2005 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CK_HK_WF157_2003 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >SWINE_ANHUI_1_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA TCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA >HONGKONG_1_97_98 ------------------------------------------------GA CCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGATA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_SHANTOU_2216_2005 ATGGAGAAAATAGTGCTTCTTCTTGCAATAATCAGCCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >PEREGRINEFALCON_HK_D0028_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HONGKONG_1_538_97 ------------------------------------------------GA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/prime-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849) |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/prime-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,391 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 4.123712641737602, 511.6499971244988, -5.608842688620929, -7.031699805798055, 1, 3.180962375542725, 1, -5.599238755695894, 0.7828049218517579, 1, -5.608352884924835, -2.115291881920681, 1, -5.604784076919627, -5.404956845857691, 1, -5.615111503355894, 2.462902938936584, 1, -5.607953657572869],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 4.849174446703908, 0.2440623951294166, -7.530855366772653, -8.547881040478554, 1, 8.833984038052169, 1, -7.53445935473729, 1.725573110573239, 1, -7.53079217870133, -0.2671292981572289, 1, -7.530980113687253, -0.4804669617756561, 1, -7.530833122267245, -0.1532486612226931, 1, -7.530868793694735],\n+ [10.63135649145974, 0, 0.7502380884715356, -7.750335490678291, -7.750335610925491, 1, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839],\n+ [0, 2.202981274414969, 0.397462976308795, -6.144243972107117, -7.361850215781605, 1, -2.763157788623757, 1, -6.146863972828472, -0.02286865932396898, 1, -6.141696705195292, 2.56489740323532, 1, -6.144140070703968, 3.673465169891661, 1, -6.162164086824393, -0.3782299185469108, 1, -6.140399389962398],\n+ [0, 6.509531966707992, 0.7279903564537584, -7.452295439546786, -8.507460649598423, 1, 6.763405786911178, 1, -7.454926555248795, 0.6678772051425989, 1, -7.451746683657063, -0.5798067642619018, 1, -7.452771449125621, -0.2211171350169704, 1, -7.452165845137638, 0.1663073214171773, 1, 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-0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 2.699658477079707, 0.4801615193392039, -5.903524182207455, -6.898872136243598, 1, -0.8716130556024849, 1, -5.903538930457988, -0.4627800379305517, 1, -5.903694932983693, 3.044105631862708, 1, -5.908943461477226, -0.07628230444039112, 1, -5.903502621374115, 0.3057953308962, 1, -5.903488680659473],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, '..b' [0.0116874925496928],\n+ [0.01921743321791434],\n+ [0.00769695150511784],\n+ [0.004704463089092132],\n+ [0.005592004637968804],\n+ [0.00919478452948895],\n+ [0.03431876246786721],\n+ [0.02097601254029597],\n+ [0.02493333610872543],\n+ [0.04099722156245031],\n+ [0.006131000492593795],\n+ [0.01198292502502543],\n+ [0.004198752217504174],\n+ [0.002566324448628536],\n+ [0.003050485878513492],\n+ [0.005015832814718212],\n+ [0.001227885122343091],\n+ [0.001459537288103269],\n+ [0.002399878352343215],\n+ [0.008957344771016727],\n+ [0.00547482958980595],\n+ [0.006507708080284218],\n+ [0.01070045135026252] \n+ ],\n+ "Log Likelihood":-277.7176481414617,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.4074296362572946, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":43\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":658.4548031196325,\n+ "Equilibrium frequencies": [\n+[0.3543689320388349],\n+ [0.1790722761596548],\n+ [0.2076591154261057],\n+ [0.2588996763754045] \n+ ],\n+ "Log Likelihood":-292.5311130078037,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0,\n+ "Substitution rate from nucleotide C to nucleotide G":0,\n+ "Substitution rate from nucleotide C to nucleotide T":1.816257034982832,\n+ "Substitution rate from nucleotide G to nucleotide T":0\n+ },\n+ "display order":0,\n+ "estimated parameters":36\n+ }\n+ },\n+ "input":{\n+ "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa",\n+ "number of sequences":13,\n+ "number of sites":50,\n+ "partition count":1,\n+ "trees":{\n+ "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "CHICKEN_CK_160_2005":"test",\n+ "CHICKEN_HEBEI_326_2005":"test",\n+ "CHICKEN_HONGKONG_915_97":"test",\n+ "CK_HK_WF157_2003":"test",\n+ "GOOSE_HONGKONG_W355_97":"test",\n+ "GOOSE_SHANTOU_2216_2005":"test",\n+ "HONGKONG_1_538_97":"test",\n+ "HONGKONG_1_97_98":"test",\n+ "HUMAN_VIETNAM_3062_2004":"test",\n+ "HUMAN_VIETNAM_CL105_2005":"test",\n+ "MALLARD_VIETNAM_16_2003":"test",\n+ "Node10":"test",\n+ "Node11":"test",\n+ "Node13":"test",\n+ "Node17":"test",\n+ "Node18":"test",\n+ "Node19":"test",\n+ "Node2":"test",\n+ "Node23":"test",\n+ "Node24":"test",\n+ "Node25":"test",\n+ "Node3":"test",\n+ "Node4":"test",\n+ "Node5":"test",\n+ "Node7":"test",\n+ "Node9":"test",\n+ "PEREGRINEFALCON_HK_D0028_2004":"test",\n+ "SWINE_ANHUI_1_2004":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "PRIME analysis":{\n+ "order":2,\n+ "timer":86\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":89\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/relax-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.fa Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>Human +AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Chimp +GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Baboon +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>RhMonkey +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Cow +------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT +>Pig +---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT +>Horse +------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT +>Cat +---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC +>Mouse +---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC +>Rat +---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/relax-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/relax-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Fri Mar 27 13:15:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795) |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/relax-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,499 @@\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+ [0.0091760343267108'..b',\n+ "k (general descriptive)":0.2294495132372282,\n+ "RELAX alternative":0.1341640738853253,\n+ "RELAX null":0.1483938193994467,\n+ "RELAX partitioned descriptive":0.1476318125310598\n+ },\n+ "Rat":{\n+ "original name":"Rat",\n+ "Nucleotide GTR":0.06669544716210057,\n+ "MG94xREV with separate rates for branch sets":0.06725647453745125,\n+ "General descriptive":0.07175915155128718,\n+ "k (general descriptive)":0.5208088414555363,\n+ "RELAX alternative":0.0724007498013708,\n+ "RELAX null":0.07365614414375878,\n+ "RELAX partitioned descriptive":0.07568744563050285\n+ },\n+ "Node1":{\n+ "Nucleotide GTR":0.2771601504028877,\n+ "MG94xREV with separate rates for branch sets":0.286127507474972,\n+ "General descriptive":0.3532216661512288,\n+ "k (general descriptive)":0.2199586786715634,\n+ "RELAX alternative":0.3833004811985787,\n+ "RELAX null":0.4576044234710181,\n+ "RELAX partitioned descriptive":0.4360897576025625\n+ },\n+ "Node12":{\n+ "Nucleotide GTR":0.01783222754921504,\n+ "MG94xREV with separate rates for branch sets":0.01799298835381691,\n+ "General descriptive":0.01771170858901891,\n+ "k (general descriptive)":0.1560499010177516,\n+ "RELAX alternative":0.01833338832069913,\n+ "RELAX null":0.01828012634520382,\n+ "RELAX partitioned descriptive":0.01877701767421286\n+ },\n+ "Node2":{\n+ "Nucleotide GTR":0.06619118337434968,\n+ "MG94xREV with separate rates for branch sets":0.06192085035608558,\n+ "General descriptive":0.05843310574046084,\n+ "k (general descriptive)":0.2816499194095207,\n+ "RELAX alternative":0.05469841675490748,\n+ "RELAX null":0.06219694236954142,\n+ "RELAX partitioned descriptive":0.06011281230238084\n+ },\n+ "Node3":{\n+ "Nucleotide GTR":0.09883746945145887,\n+ "MG94xREV with separate rates for branch sets":0.09744342239018626,\n+ "General descriptive":0.1340338084149808,\n+ "k (general descriptive)":0.8358980179450297,\n+ "RELAX alternative":0.1164056814082033,\n+ "RELAX null":0.1282588343299434,\n+ "RELAX partitioned descriptive":0.1194563668460339\n+ },\n+ "Node8":{\n+ "Nucleotide GTR":0.106110061225871,\n+ "MG94xREV with separate rates for branch sets":0.1090208137603471,\n+ "General descriptive":0.1401594332730181,\n+ "k (general descriptive)":0.9135621448569878,\n+ "RELAX alternative":0.1275155316795084,\n+ "RELAX null":0.1346842719904758,\n+ "RELAX partitioned descriptive":0.1358683972849559\n+ },\n+ "Node9":{\n+ "Nucleotide GTR":0.02567391471029082,\n+ "MG94xREV with separate rates for branch sets":0.02582385148170195,\n+ "General descriptive":0.02665352479510937,\n+ "k (general descriptive)":0.1089752436854629,\n+ "RELAX alternative":0.02681134359856903,\n+ "RELAX null":0.02759760291393045,\n+ "RELAX partitioned descriptive":0.02746061131173372\n+ }\n+ },\n+ "attributes":{\n+ "original name":{\n+ "attribute type":"node label",\n+ "display order":-1\n+ },\n+ "Nucleotide GTR":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ },\n+ "MG94xREV with separate rates for branch sets":{\n+ "attribute type":"branch length",\n+ "display order":1\n+ },\n+ "General descriptive":{\n+ "attribute type":"branch length",\n+ "display order":4\n+ },\n+ "k (general descriptive)":{\n+ "attribute type":"branch label",\n+ "display order":4\n+ },\n+ "RELAX alternative":{\n+ "attribute type":"branch length",\n+ "display order":2\n+ },\n+ "RELAX null":{\n+ "attribute type":"branch length",\n+ "display order":3\n+ },\n+ "RELAX partitioned descriptive":{\n+ "attribute type":"branch length",\n+ "display order":5\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/slac-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slac-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,2076 @@\n+{\n+ "analysis":{\n+ "info":"SLAC (Single Likelihood Ancestor Counting)\\n uses a maximum likelihood ancestral state reconstruction\\n and minimum path substitution counting to estimate site - level\\n dS and dN,\\n and applies a simple binomial - based test to test\\n if dS differs drom dN.\\n The estimates aggregate information over all branches,\\n so the signal is derived from\\n pervasive diversification or conservation. A subset of branches can be selected\\n for testing as well.\\n Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n+ "version":"2.00",\n+ "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",\n+ "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-3531.963798530155,\n+ "estimated parameters":24,\n+ "AIC-c":7112.142458295762,\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":0.5474490057204714,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378\n+ },\n+ "display order":0\n+ },\n+ "Global MG94xREV":{\n+ "Log Likelihood":-3466.724829119623,\n+ "estimated parameters":31,\n+ "AIC-c":6996.52909240682,\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+ [0.009176034326710849],\n+ [0.007500393094996483],\n+ [0.00928511773266342],\n+ [0.007803986567571961],\n+ [0.00784869593340758],\n+ [0.009716299514778986],\n+ [0.008166387662818644],\n+ [0.01412467213650941],\n+ [0.01154535713247913],\n+ [0.01429258425298098],\n+ [0.01201267864744234]\n+ ],\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*":[\n+ [0.9952474740528205, 1]\n+ ]\n+ }'..b' 0.7667128671748024, 0.890841230650352, 0.8320854747642759, 1.723419162497329],\n+ [1, 2, 5, 0.4749999999999517, 0.3333333333333333, 5, 0.2374999999999758, -2.183160128350873, 1, 0.03782959914646881, 1.723419162497329],\n+ [0.843656832841698, 2.408185306598483, 2.938888888888878, 9.886111111111106, 0.2843369743316476, 4.574922684961112, 4.238621782785534, 1.594080406346652, 0.7883087325663475, 0.9345721380406598, 1.723419162497329],\n+ [0.4015666212427145, 2.598433378757286, 0, 0.4749999999999517, 0.1338555404142381, 0, 0.1828024546956531, 0.1060696426461699, 1, 1, 1.723419162497329],\n+ [0.7631315455164901, 2.303416321948652, 4, 8.579166666666659, 0.2598642419466547, 6.13519119941088, 3.924250265172389, 0.9761043336904643, 0.9485561128462242, 0.8823115672560321, 1.723419162497329],\n+ [1, 2, 0, 2, 0.3333333333333333, 0, 1, 0.5802418945783016, 0.6666666666666667, 1, 1.723419162497329],\n+ [0.5108071114874615, 2.57138242847146, 2, 3, 0.1702690371624872, 4.689333452586883, 1.205209935254436, -0.4366182159717286, 0.989584442823033, 0.5260318186931501, 1.723419162497329],\n+ [0.7355430390802056, 2.24582979842974, 0.5, 7.5, 0.2547488097891927, 0.6797698753634438, 3.49464769706217, 1.865065863585222, 0.2612708950448336, 1, 1.723419162497329],\n+ [0.6267060118898431, 2.238010426610814, 2, 2, 0.2199736580517843, 3.214404615308581, 0.9115992408219742, -0.4173100575643724, 0.9651119805840197, 0.5225975649035184, 1.723419162497329],\n+ [0.9101251033652521, 2.317095536064913, 2, 7.158333333333317, 0.303375034455084, 2.290533001213371, 3.425698572354657, 1.350172793073417, 0.6586555929582461, 0.9471075623091124, 1.723419162497329],\n+ [0.673672140559856, 2.489920391149622, 2.158333333333317, 8.13194444444443, 0.226629447539539, 4.126852101032075, 3.54552687644596, 1.976804163754458, 0.836071480785966, 1, 1.723419162497329],\n+ [0.6897615550532064, 2.790263254042777, 2.333333333333333, 8.526388888888887, 0.2304358158933025, 6.094648833588598, 3.276393298181066, 0.3613328345356598, 0.9231255898428308, 0.6686732177677085, 1.723419162497329],\n+ [0.7946586568361008, 2.167975169364766, 1, 6, 0.2715103527844899, 1.405104306225133, 2.818037808360176, 0.8363424597513123, 0.7430921944460164, 0.8718081545299928, 1.723419162497329],\n+ [0.925309922046851, 2.236871623721474, 2.579166666666659, 8.5, 0.3084366406822837, 2.925882077362623, 4.049552410687498, 1.364532301558911, 0.6461765519656628, 0.9254887173196068, 1.723419162497329],\n+ [0.9581686586422306, 2.13880638531327, 2, 5, 0.3193895528807435, 2.322358138625455, 2.415212293435113, 0.7773494920126088, 0.7795378572552829, 0.8920156958059355, 1.723419162497329],\n+ [0.7593283298052359, 2.460727196465021, 3, 8.526388888888887, 0.253391086431764, 4.622736289498208, 3.556429743974461, 1.477112310794914, 0.8989574146760382, 0.8927015041979159, 1.723419162497329],\n+ [0.5112602866741613, 2.217104081344285, 0, 0, 0.1873871000028779, 0, 0, 0, 1, 1, 1.723419162497329],\n+ [1, 1.952467466533022, 2, 4, 0.342663635137335, 2, 2.086372572382543, 0.63035887961715, 0.7821097289668139, 0.8770423554138478, 1.723419162497329],\n+ [0.75154665371034, 2.194207467544889, 0.7374999999999758, 2.895833333333293, 0.2591620486295864, 1.086891717767276, 1.342183608392251, 0.6579931372011264, 0.7050462382636092, 1, 1.723419162497329],\n+ [0.6018431830315369, 2.241218884393843, 1, 2, 0.2148519149742012, 1.661562393982619, 0.9093567672257744, -0.4364612179818503, 0.8845364432183682, 0.5159895622684771, 1.723419162497329],\n+ [1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 1.723419162497329],\n+ [1.401566621242714, 1.598433378757286, 0, 0, 0.4671888737475713, 0, 0, 0, 1, 1, 1.723419162497329],\n+ [0.5861816684921827, 2.463353001049777, 3, 4.158333333333317, 0.1963715666467496, 5.590266983451943, 1.70370382635879, -1.259842549492376, 0.9887093275905696, 0.2624813117321075, 1.723419162497329]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/sm19-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in1.nhx Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| @@ -0,0 +1,152 @@ +#NEXUS +begin taxa; + dimensions ntax=50; + taxlabels + C019-B2_10_1[&!color=#ff0000] + C019-B2_13_1[&!color=#ff0000] + C019-B2_16_1[&!color=#ff0000] + C019-B2_17_3[&!color=#ff0000] + C019-B2_18_1[&!color=#ff0000] + C019-B2_1_2[&!color=#ff0000] + C019-B2_24_1[&!color=#ff0000] + C019-B2_28_1[&!color=#ff0000] + C019-B2_29_1[&!color=#ff0000] + C019-B2_31_1[&!color=#ff0000] + C019-B2_32_1[&!color=#ff0000] + C019-B2_34_1[&!color=#ff0000] + C019-B2_35_1[&!color=#ff0000] + C019-B2_42_2[&!color=#ff0000] + C019-B2_43_2[&!color=#ff0000] + C019-B2_45_1[&!color=#ff0000] + C019-B2_46_2[&!color=#ff0000] + C019-B2_47_3[&!color=#ff0000] + C019-B2_4_1[&!color=#ff0000] + C019-B2_52_1[&!color=#ff0000] + C019-B2_53_1[&!color=#ff0000] + C019-B2_54_1[&!color=#ff0000] + C019-B2_5_1[&!color=#ff0000] + C019-B2_6_3[&!color=#ff0000] + C019-B2_9_1[&!color=#ff0000] + C019-S2_10_1[&!color=#0000ff] + C019-S2_11_1[&!color=#0000ff] + C019-S2_12_2[&!color=#0000ff] + C019-S2_13_1[&!color=#0000ff] + C019-S2_14_1[&!color=#0000ff] + C019-S2_15_4[&!color=#0000ff] + C019-S2_16_1[&!color=#0000ff] + C019-S2_17_1[&!color=#0000ff] + C019-S2_18_2[&!color=#0000ff] + C019-S2_19_1[&!color=#0000ff] + C019-S2_1_1[&!color=#0000ff] + C019-S2_20_2[&!color=#0000ff] + C019-S2_21_1[&!color=#0000ff] + C019-S2_22_1[&!color=#0000ff] + C019-S2_23_2[&!color=#0000ff] + C019-S2_24_1[&!color=#0000ff] + C019-S2_25_2[&!color=#0000ff] + C019-S2_2_1[&!color=#0000ff] + C019-S2_3_1[&!color=#0000ff] + C019-S2_4_1[&!color=#0000ff] + C019-S2_5_1[&!color=#0000ff] + C019-S2_6_1[&!color=#0000ff] + C019-S2_7_1[&!color=#0000ff] + C019-S2_8_1[&!color=#0000ff] + C019-S2_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] ((((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773):9.4E-4,((((((C019-B2_28_1:0.002896,C019-B2_29_1:9.09E-4):0.004372,C019-B2_31_1:0.003387):0.001252,C019-S2_9_1:0.001965):4.28E-4,C019-B2_34_1:0.003365):0.00173,C019-S2_2_1:0.011763):5.94E-4,((((C019-B2_4_1:0.002924,C019-B2_6_3:8.81E-4):0.001821,C019-B2_5_1:0.001994):0.006052,C019-S2_1_1:0.011533):0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696):0.001115,C019-S2_7_1:0.004624):0.003256):0.001452):0.002006):3.96E-4,((C019-S2_10_1:0.005429,C019-S2_12_2:3.52E-4):9.31E-4,C019-B2_42_2:9.87E-4):6.51E-4):5.28E-4,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151):0.002202):3.98E-4,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149):0.003701,C019-B2_1_2:0.011845):0.001658,C019-S2_3_1:0.009874):1.58E-4,C019-S2_5_1:0.009998):2.67E-4,(((C019-B2_17_3:0.0,C019-S2_22_1:0.0):6.76E-4,C019-B2_16_1:0.003129):2.62E-4,(((((C019-B2_18_1:0.0,C019-S2_25_2:0.0):3.0E-5,C019-S2_24_1:-3.0E-5):7.69E-4,C019-S2_23_2:0.003047):4.93E-4,(((((C019-B2_24_1:0.004304,C019-S2_19_1:-0.002103):0.00459,C019-S2_17_1:0.00129):0.002822,C019-S2_18_2:0.004477):8.52E-4,C019-S2_21_1:0.001446):8.3E-4,C019-S2_20_2:0.003028):0.002252):0.001275,C019-B2_13_1:0.006181):9.2E-4):0.003349):0.001411,C019-S2_13_1:-4.68E-4):0.001963):3.46E-4,(((C019-B2_45_1:8.37E-4,C019-S2_8_1:0.006794):0.001393,C019-S2_14_1:5.17E-4):3.77E-4,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995):9.13E-4,C019-S2_11_1:0.002993):5.52E-4,(((C019-B2_46_2:0.0,C019-S2_15_4:0.0):0.001576,C019-S2_16_1:0.002229):0.001073,C019-B2_47_3:8.77E-4):8.62E-4):7.32E-4):3.46E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/sm19-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in2.nhx Fri Mar 27 13:15:01 2020 -0400 |
| [ |
| @@ -0,0 +1,166 @@ +#NEXUS +begin taxa; + dimensions ntax=64; + taxlabels + C019-B3_103_1[&!color=#ff0000] + C019-B3_10_1[&!color=#ff0000] + C019-B3_121_1[&!color=#ff0000] + C019-B3_122_4[&!color=#ff0000] + C019-B3_125_1[&!color=#ff0000] + C019-B3_132_1[&!color=#ff0000] + C019-B3_140_2[&!color=#ff0000] + C019-B3_144_1[&!color=#ff0000] + C019-B3_147_1[&!color=#ff0000] + C019-B3_154_1[&!color=#ff0000] + C019-B3_162_1[&!color=#ff0000] + C019-B3_164_1[&!color=#ff0000] + C019-B3_173_1[&!color=#ff0000] + C019-B3_179_1[&!color=#ff0000] + C019-B3_180_1[&!color=#ff0000] + C019-B3_18_1[&!color=#ff0000] + C019-B3_1_1[&!color=#ff0000] + C019-B3_201_1[&!color=#ff0000] + C019-B3_211_4[&!color=#ff0000] + C019-B3_26_6[&!color=#ff0000] + C019-B3_27_1[&!color=#ff0000] + C019-B3_32_1[&!color=#ff0000] + C019-B3_37_1[&!color=#ff0000] + C019-B3_3_2[&!color=#ff0000] + C019-B3_57_1[&!color=#ff0000] + C019-B3_59_1[&!color=#ff0000] + C019-B3_61_3[&!color=#ff0000] + C019-B3_63_1[&!color=#ff0000] + C019-B3_84_1[&!color=#ff0000] + C019-B3_87_1[&!color=#ff0000] + C019-B3_94_1[&!color=#ff0000] + C019-B3_98_1[&!color=#ff0000] + C019-S3_10_3[&!color=#0000ff] + C019-S3_11_1[&!color=#0000ff] + C019-S3_12_1[&!color=#0000ff] + C019-S3_13_1[&!color=#0000ff] + C019-S3_14_1[&!color=#0000ff] + C019-S3_15_1[&!color=#0000ff] + C019-S3_16_1[&!color=#0000ff] + C019-S3_17_1[&!color=#0000ff] + C019-S3_18_1[&!color=#0000ff] + C019-S3_19_2[&!color=#0000ff] + C019-S3_1_3[&!color=#0000ff] + C019-S3_20_1[&!color=#0000ff] + C019-S3_21_1[&!color=#0000ff] + C019-S3_22_2[&!color=#0000ff] + C019-S3_23_6[&!color=#0000ff] + C019-S3_24_1[&!color=#0000ff] + C019-S3_25_1[&!color=#0000ff] + C019-S3_26_1[&!color=#0000ff] + C019-S3_27_1[&!color=#0000ff] + C019-S3_28_1[&!color=#0000ff] + C019-S3_29_1[&!color=#0000ff] + C019-S3_2_1[&!color=#0000ff] + C019-S3_30_5[&!color=#0000ff] + C019-S3_31_1[&!color=#0000ff] + C019-S3_32_1[&!color=#0000ff] + C019-S3_3_1[&!color=#0000ff] + C019-S3_4_1[&!color=#0000ff] + C019-S3_5_1[&!color=#0000ff] + C019-S3_6_1[&!color=#0000ff] + C019-S3_7_44[&!color=#0000ff] + C019-S3_8_1[&!color=#0000ff] + C019-S3_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] (((((((C019-S3_30_5:0.001628,C019-S3_29_1:0.006003):0.00113,(C019-B3_173_1:0.001171,C019-S3_28_1:0.002634):0.001744):8.3E-4,C019-B3_132_1:0.014016):5.86E-4,((C019-S3_25_1:0.002323,C019-S3_26_1:0.001482):9.35E-4,C019-B3_144_1:0.004793):0.001476):5.2E-4,((C019-B3_140_2:0.005006,C019-B3_211_4:7.09E-4):0.005792,C019-S3_24_1:0.003793):6.51E-4):3.29E-4,((((((C019-B3_180_1:0.007012,C019-S3_12_1:0.002539):0.001059,C019-B3_164_1:0.004685):0.001059,C019-B3_201_1:0.002755):4.7E-4,C019-S3_27_1:0.004308):5.29E-4,(C019-B3_179_1:0.00111,C019-B3_162_1:0.006521):0.001397):4.5E-4,(((C019-B3_98_1:0.00603,C019-B3_84_1:0.011255):0.001462,C019-B3_3_2:0.01022):0.004778,(((((C019-B3_122_4:-1.5E-5,C019-B3_121_1:0.003821):1.07E-4,(((C019-S3_6_1:3.19E-4,C019-S3_5_1:0.003493):2.06E-4,C019-S3_4_1:0.003609):1.56E-4,C019-S3_7_44:-1.63E-4):0.001868):8.3E-5,C019-S3_2_1:0.003743):9.49E-4,C019-S3_3_1:9.47E-4):1.32E-4,((((((C019-B3_87_1:0.004026,C019-B3_94_1:0.003649):0.001868,C019-S3_9_1:0.001947):5.6E-5,C019-S3_8_1:0.001847):0.002662,C019-S3_10_3:0.003074):0.001087,C019-B3_103_1:0.002733):2.29E-4,(C019-S3_1_3:0.003978,C019-B3_125_1:0.003697):9.13E-4):4.97E-4):0.006645):7.82E-4):8.25E-4):5.47E-4,((((C019-S3_22_2:9.84E-4,C019-S3_23_6:0.005041):0.001644,(((((((((C019-B3_32_1:0.001955,C019-S3_15_1:-5.5E-5):9.11E-4,C019-B3_37_1:9.97E-4):0.001209,C019-B3_57_1:0.002666):0.001047,C019-B3_59_1:0.001825):0.001321,(C019-B3_26_6:-2.4E-5,C019-B3_27_1:2.4E-5):0.006853):0.001793,C019-B3_10_1:0.009272):0.001166,((C019-S3_19_2:7.58E-4,C019-S3_17_1:0.003048):0.001952,C019-S3_11_1:0.007625):0.001734):0.001109,C019-B3_147_1:0.00437):0.001515,(((C019-S3_32_1:0.009024,C019-S3_31_1:0.002453):0.007605,C019-B3_1_1:0.014729):0.003341,(C019-S3_14_1:0.002908,C019-S3_13_1:0.004722):0.006888):0.001642):0.00149):2.85E-4,(((C019-S3_20_1:4.17E-4,C019-S3_21_1:0.001505):0.001098,C019-S3_16_1:0.00369):0.00156,((C019-B3_61_3:7.33E-4,C019-B3_63_1:0.006898):0.003303,C019-B3_18_1:0.0063):0.00288):7.85E-4):1.97E-4,(C019-S3_18_1:3.32E-4,C019-B3_154_1:0.00368):0.001664):5.47E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/sm19-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out1.json Fri Mar 27 13:15:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,2606 @@\n+{\n+ "compartments":2,\n+ "events":{\n+ "C019-B2_18_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_24_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_45_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_46_2":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_47_3":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-S2_1_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_22_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_2_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_9_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node2":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node28":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node34":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node45":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node52":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node59":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node88":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ }\n+ },\n+ "leaf-count":50,\n+ "migrations":16,\n+ "node-migrations":{\n+ "Node10":1,\n+ "Node11":1,\n+ "Node12":0,\n+ "Node13":0,\n+ "Node2":6,\n+ "Node20":2,\n+ "Node21":1,\n+ "Node22":0,\n+ "Node23":0,\n+ "Node28":1,\n+ "Node29":0,\n+ "Node3":5,\n+ "Node33":1,\n+ "Node34":1,\n+ "Node38":0,\n+ "Node4":4,\n+ "Node41":6,\n+ "Node42":6,\n+ "Node43":1,\n+ "Node44":1,\n+ "Node45":1,\n+ "Node46":0,\n+ "Node5":0,\n+ "Node52":5,\n+ "Node53":1,\n+ "Node54":1,\n+ "Node58":3,\n+ "Node59":3,\n+ "Node60":1,\n+ "Node61":1,\n+ "Node62":1,\n+ "Node67":1,\n+ "Node68":1,\n+ "Node69":1,\n+ "Node70":1,\n+ "Node71":1,\n+ "Node79":16,\n+ "Node8":4,\n+ "Node80":4,\n+ "Node81":1,\n+ "Node82":1,\n+ "Node86":3,\n+ "Node87":1,\n+ "Node88":1,\n+ "Node9":2,\n+ "Node92":2,\n+ "Node93":1,\n+ "Node94":1\n+ },\n+ "node-p-value":{\n+ "panmictic":{\n+ "Node10":0.3866133866133866,\n+ "Node11":0.6103896103896104,\n+ "Node12":0.1568431568431568,\n+ "Node13":0.3486513486513487,\n+ "Node2":0.4045954045954046,\n+ "Node20":0.5954045954045954,\n+ "Node21":0.6183816183816184,\n+ "Node22":0.1538461538461539,\n+ "Node23":0.3626373626373626,\n+ "Node28":0.9050949050949051,\n+ "Node29":0.3786213786213786,\n+ "Node3":0.2897102897102897,\n+ "Node33":0.8901098901098901,\n+ "Node34":1,\n+ "Node38":0.3966033966033966,\n+ "Node4":0.2787212787212787,\n+ "Node41":0.3816183816183816,\n+ "Node42":0.4715284715284715,\n+ "Node43":0.3926073926073926,\n+ "Node44":0.6113886113886113,\n+ "Node45":0.8561438561438561,\n+ "Node46":0.4015984015984016,\n+ "Node5":0.3886113886113886,\n+ "Node52":0.7592407592407593,\n+ "Node53":0.8971028971028971,\n+ "Node54":1,\n+ "Node58":0.3706293706293706,\n+ "Node59":0.5024975024975025,\n+ "Node60":0.5954045954045954,\n+ "Node61":0.8671328671328671,\n+ "Node62":1,\n+ "Node67":0.2117882117882118,\n+ "Node68":0.3646353646353646,\n+ "Node69":0.5784215784215784,\n+ "Node70":0.8501498501498501,\n+ "Node71":1,\n+ "Node79":0.3846153846153846,\n+ "Node8":0.5424575424575424,\n+ "Node80":0.926073926073926,\n+ "Node81":0.8901098901098901,\n+ "Node82":1,\n+ "Node86":0.967032967032967,\n+ "Node87":0.8901098901098901,\n+ "Node88":1,\n+ "Node9":0.7902097902097902,\n+ "Node92":1,\n+ "Node93":0.8721278721278721,\n+ "Node94":1\n+ },\n+ "structured":{\n+ "Node10":0.935064935064935,\n+ "Node11":1,\n+ "Node12":0.8671328671328671,\n+ "Node13":1,\n+ "Node2":0.7232767232767233,\n+ "Node20":0.9760239760239761,\n+ "Node21":1,\n+ "Node22":0.8731268731268731,\n+ "Node23":1,\n+ "Node28":0.9050949050949051,\n+ "Node29":1,\n+ "Node3":0.9100899100899101,\n+ "Node33":1,\n+ "Node34":1,\n+ "Node38":1,\n+ "Node4":0.936063936063936,\n+ "Node41":0.70'..b'1:0.001994)0.1538461538461539:0.006052,C019-S2_1_1:0.011533)0.6183816183816184:0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696)0.3786213786213786:0.001115,C019-S2_7_1:0.004624)0.9050949050949051:0.003256)0.5954045954045954:0.001452)0.5424575424575424:0.002006)0.2787212787212787:0.000396,((C019-S2_10_1:0.005429,C019-S2_12_2:0.000352)1:0.000931,C019-B2_42_2:0.000987)0.8901098901098901:0.000651)0.2897102897102897:0.000528,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151)0.3966033966033966:0.002202)0.4045954045954046:0.000398,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149)0.4015984015984016:0.003701,C019-B2_1_2:0.011845)0.8561438561438561:0.001658,C019-S2_3_1:0.009874000000000001)0.6113886113886113:0.000158,C019-S2_5_1:0.009998)0.3926073926073926:0.000267,(((C019-B2_17_3:1e-10,C019-S2_22_1:1e-10)1:0.000676,C019-B2_16_1:0.003129)0.8971028971028971:0.000262,(((((C019-B2_18_1:1e-10,C019-S2_25_2:1e-10)1:3e-05,C019-S2_24_1:1e-10)0.8671328671328671:0.000769,C019-S2_23_2:0.003047)0.5954045954045954:0.0004929999999999999,(((((C019-B2_24_1:0.004304,C019-S2_19_1:1e-10)1:0.00459,C019-S2_17_1:0.00129)0.8501498501498501:0.002822,C019-S2_18_2:0.004477)0.5784215784215784:0.000852,C019-S2_21_1:0.001446)0.3646353646353646:0.00083,C019-S2_20_2:0.003028)0.2117882117882118:0.002252)0.5024975024975025:0.001275,C019-B2_13_1:0.006181)0.3706293706293706:0.00092)0.7592407592407593:0.003349)0.4715284715284715:0.001411,C019-S2_13_1:1e-10)0.3816183816183816:0.001963,(((C019-B2_45_1:0.000837,C019-S2_8_1:0.006794)1:0.001393,C019-S2_14_1:0.000517)0.8901098901098901:0.000377,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995)1:0.000913,C019-S2_11_1:0.002993)0.8901098901098901:0.000552,(((C019-B2_46_2:1e-10,C019-S2_15_4:1e-10)1:0.001576,C019-S2_16_1:0.002229)0.8721278721278721:0.001073,C019-B2_47_3:0.000877)1:0.000862)0.967032967032967:0.000732)0.926073926073926:0.000346)0.3846153846153846",\n+ "tree-p-structured":"(((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773)1:0.00094,((((((C019-B2_28_1:0.002896,C019-B2_29_1:0.000909)1:0.004372,C019-B2_31_1:0.003387)0.8671328671328671:0.001252,C019-S2_9_1:0.001965)1:0.000428,C019-B2_34_1:0.003365)0.935064935064935:0.00173,C019-S2_2_1:0.011763)0.7902097902097902:0.000594,((((C019-B2_4_1:0.002924,C019-B2_6_3:0.0008809999999999999)1:0.001821,C019-B2_5_1:0.001994)0.8731268731268731:0.006052,C019-S2_1_1:0.011533)1:0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696)1:0.001115,C019-S2_7_1:0.004624)0.9050949050949051:0.003256)0.9760239760239761:0.001452)0.8871128871128872:0.002006)0.936063936063936:0.000396,((C019-S2_10_1:0.005429,C019-S2_12_2:0.000352)1:0.000931,C019-B2_42_2:0.000987)1:0.000651)0.9100899100899101:0.000528,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151)1:0.002202)0.7232767232767233:0.000398,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149)1:0.003701,C019-B2_1_2:0.011845)0.8561438561438561:0.001658,C019-S2_3_1:0.009874000000000001)1:0.000158,C019-S2_5_1:0.009998)0.9410589410589411:0.000267,(((C019-B2_17_3:1e-10,C019-S2_22_1:1e-10)1:0.000676,C019-B2_16_1:0.003129)1:0.000262,(((((C019-B2_18_1:1e-10,C019-S2_25_2:1e-10)1:3e-05,C019-S2_24_1:1e-10)0.8671328671328671:0.000769,C019-S2_23_2:0.003047)1:0.0004929999999999999,(((((C019-B2_24_1:0.004304,C019-S2_19_1:1e-10)1:0.00459,C019-S2_17_1:0.00129)0.8501498501498501:0.002822,C019-S2_18_2:0.004477)1:0.000852,C019-S2_21_1:0.001446)0.929070929070929:0.00083,C019-S2_20_2:0.003028)0.7602397602397603:0.002252)0.9170829170829171:0.001275,C019-B2_13_1:0.006181)0.8061938061938062:0.00092)0.7592407592407593:0.003349)0.8021978021978022:0.001411,C019-S2_13_1:1e-10)0.7002997002997003:0.001963,(((C019-B2_45_1:0.000837,C019-S2_8_1:0.006794)1:0.001393,C019-S2_14_1:0.000517)1:0.000377,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995)1:0.000913,C019-S2_11_1:0.002993)0.8901098901098901:0.000552,(((C019-B2_46_2:1e-10,C019-S2_15_4:1e-10)1:0.001576,C019-S2_16_1:0.002229)1:0.001073,C019-B2_47_3:0.000877)1:0.000862)0.967032967032967:0.000732)1:0.000346)0.7822177822177823"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 725ef5f6d749 test-data/sm19-out2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out2.json Fri Mar 27 13:15:01 2020 -0400 |
| b |
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No newline at end of file\n' |