Repository 'hyphy_conv'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/hyphy_conv

Changeset 11:beeeed9665ea (2023-03-02)
Previous changeset 10:6761212b7f1d (2022-08-18)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
modified:
hyphy_conv.xml
macros.xml
test-data/absrel-in1.fa
test-data/absrel-in1.nhx
test-data/conv-out1.nex
test-data/relax-in1.nhx
removed:
test-data/absrel-out1.json
test-data/absrel-out2.json
test-data/busted-out1.json
test-data/busted-out2-1.json
test-data/busted-out2-2.json
test-data/slac-out1.json
b
diff -r 6761212b7f1d -r beeeed9665ea hyphy_conv.xml
--- a/hyphy_conv.xml Thu Aug 18 14:02:04 2022 +0000
+++ b/hyphy_conv.xml Thu Mar 02 15:10:54 2023 +0000
b
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="hyphy_conv" name="HyPhy-Conv" version="@TOOL_VERSION@+galaxy1" profile="19.09">
+<tool id="hyphy_conv" name="HyPhy-Conv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>translate an in-frame codon alignment to proteins</description>
     <macros>
         <import>macros.xml</import>
b
diff -r 6761212b7f1d -r beeeed9665ea macros.xml
--- a/macros.xml Thu Aug 18 14:02:04 2022 +0000
+++ b/macros.xml Thu Mar 02 15:10:54 2023 +0000
[
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.5.36</token>
+    <token name="@TOOL_VERSION@">2.5.47</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+
     <xml name="inputs">
      <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
         <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
@@ -10,8 +13,8 @@
             <xref type="bio.tools">HyPhy</xref>
         </xrefs>
     </xml>
-    <xml name="substitution">
-        <param name="model" type="select" label="Substitution model">
+    <xml name="substitution" tokens="argument">
+        <param argument="@ARGUMENT@" type="select" label="Substitution model">
             <option value="GTR">GTR - General time reversible
             model</option>
             <option value="LG">LG - Generalist empirical model from
@@ -66,13 +69,13 @@
 
     <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="--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">
+        <param argument="--code" name="gencodeid" type="select" label="Genetic code">
             <option value="Universal">Universal code</option>
             <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
             code</option>
@@ -119,7 +122,7 @@
 
     <xml name="branches">
         <conditional name="branch_cond">
-            <param name="branch_sel" type="select" label="Set of branches to test">
+            <param argument="--branches" name="branch_sel" type="select" label="Set of branches to test">
                 <option value="All">All branches</option>
                 <option value="Internal">Internal branches</option>
                 <option value="Leaves">Leaf branches</option>
@@ -152,7 +155,7 @@
         </requirements>
     </xml>
     <xml name="alternative_model_output">
-        <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
+        <data name="alternative_model" format="nhx" from_work_dir="alternative_model.nhx" label="${tool.name} on ${on_string}: Alternative model">
             <filter>advanced['save_alternative_model']</filter>
         </data>
     </xml>
@@ -188,7 +191,7 @@
             --rates $advanced.rates
             --srv $advanced.srv
             #if $advanced.save_alternative_model:
-                --save-fit alternative_model.json
+                --save-fit alternative_model.nhx
             #end if
         #end if
     ]]></token>
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/absrel-in1.fa
--- a/test-data/absrel-in1.fa Thu Aug 18 14:02:04 2022 +0000
+++ b/test-data/absrel-in1.fa Thu Mar 02 15:10:54 2023 +0000
b
@@ -1,20 +1,8 @@
->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 6761212b7f1d -r beeeed9665ea test-data/absrel-in1.nhx
--- a/test-data/absrel-in1.nhx Thu Aug 18 14:02:04 2022 +0000
+++ b/test-data/absrel-in1.nhx Thu Mar 02 15:10:54 2023 +0000
b
@@ -1,1 +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
+(((Pig:0.147969,Cow:0.21343):0.085099,Baboon:0.011873):0.340802,Rat:0.050958);
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/absrel-out1.json
--- a/test-data/absrel-out1.json Thu Aug 18 14:02:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,478 +0,0 @@\n-{\n- "analysis":{\n-   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",\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. v2.2 adds support for multiple-hit models",\n-   "contact":"spond@temple.edu",\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-   "requirements":"in-frame codon alignment and a phylogenetic tree",\n-   "version":"2.2"\n-  },\n- "branch attributes":{\n-   "0":{\n-     "Baboon":{\n-       "Baseline MG94xREV":0.001816807585564731,\n-       "Baseline MG94xREV omega ratio":0,\n-       "Corrected P-value":1,\n-       "Full adaptive model":0.001810407118394509,\n-       "LRT":0,\n-       "Nucleotide GTR":0.001678881906620672,\n-       "Rate Distributions":        [\n-[0, 1] \n-        ],\n-       "Rate classes":1,\n-       "Uncorrected P-value":1,\n-       "original name":"Baboon",\n-       "rate at which 2 nucleotides are changed instantly within a single codon":0\n-      },\n-     "Cat":{\n-       "Baseline MG94xREV":0.2286001363527903,\n-       "Baseline MG94xREV omega ratio":1.403298474422089,\n-       "Corrected P-value":1,\n-       "Full adaptive model":0.1219386838393392,\n-       "LRT":1.644967676056694,\n-       "Nucleotide GTR":0.265904547400163,\n-       "Rate Distributions":        [\n-[0.2130519766306851, 0.6352283641519592],\n-        [2.628217450705319, 0.3647716358480408] \n-        ],\n-       "Rate classes":2,\n-       "Uncorrected P-value":0.171730764045231,\n-       "original name":"Cat",\n-       "rate at which 2 nucleotides are changed instantly within a single codon":0\n-      },\n-     "Chimp":{\n-       "Baseline MG94xREV":0.001840311209746262,\n-       "Baseline MG94xREV omega ratio":10000000000,\n-       "Corrected P-value":1,\n-       "Full adaptive model":0.001841979303044237,\n-       "LRT":0.6159123786974305,\n-       "Nucleotide GTR":0.001816713800925801,\n-       "Rate Distributions":        [\n-[10000000000, 1] \n-        ],\n-       "Rate classes":1,\n-       "Uncorrected P-value":0.3069983227523322,\n-       "original name":"Chimp",\n-       "rate at which 2 nucleotides are changed instantly within a single codon":0\n-      },\n-     "Cow":{\n-       "Baseline MG94xREV":0.2070244948790512,\n-       "Baseline MG94xREV omega ratio":2.153434974462683,\n-       "Corrected P-value":0.5006146299996015,\n-       "Full adaptive model":0.1241125417707662,\n-       "LRT":4.898194538953248,\n-       "Nucleotide GTR":0.2481512612523618,\n-       "Rate Distributions":        [\n-[0, 0.52318726440949],\n-        [2.444056517734385, 0.47681273559051] \n-        ],\n-       "Rate classes":2,\n-       "Uncorrected P-value":0.03128841437497509,\n-       "original name":"Cow",\n-       "rate at which 2 nucleotides are changed instantly within a single codon":0\n-      },\n-     "Horse":{\n-       "Baseline MG94xREV":0.190365915457708,\n-       "Baseline MG94xREV omega ratio":1.182933895494305,\n-       "Corrected P-value":1,\n-       "Full adaptive model":0.0869489794025302,\n-       "LRT":2.047309801283518,\n-       "Nucleotide GTR":0.2090927256979082,\n-       "Rate Distributions":        [\n-[0, 0.5397658078247131],\n-        [1.633257246666139, 0.4602341921752869] \n-        ],\n-       "Rate classes":2,\n-       "Uncorrected P-value":0.1382789032066179,\n-       "original name":"Horse",\n-       "rate at which 2 nucleotides are changed instantly within a single codon":0\n-      },\n-     "Human":{\n-       "Baseline MG94xREV":0,\n-       "Baseline MG94xREV omega ratio":1,\n-       "Corrected P-value":1,\n-       "Full adaptive model":0,\n-       "LRT":0,\n-       "Nucle'..b'\n-      [0.005501589790395056],\n-      [0.009655668202293983],\n-      [0.007888099278638223],\n-      [0.009797203904398108],\n-      [0.008223514024394991],\n-      [0.03326722643528176],\n-      [0.02717732003095303],\n-      [0.03375486749252685],\n-      [0.02833294365668738],\n-      [0.01236215156074466],\n-      [0.01009913314808799],\n-      [0.01254335971371867],\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":-3427.720059001285,\n-     "Rate Distributions":{\n-       "Per-branch delta":{\n-         "2.5%":0,\n-         "97.5%":12.07373117808175,\n-         "Mean":1.277646334033236,\n-         "Median":0.4551223038316586\n-        },\n-       "Per-branch omega":{\n-         "2.5%":0,\n-         "97.5%":2.153434974462683,\n-         "Mean":666666667.5119981,\n-         "Median":1\n-        }\n-      },\n-     "display order":1,\n-     "estimated parameters":62\n-    },\n-   "Full adaptive model":{\n-     "AIC-c":6972.859938351839,\n-     "Log Likelihood":-3415.824749853321,\n-     "Rate Distributions":{\n-      },\n-     "display order":2,\n-     "estimated parameters":68\n-    },\n-   "Nucleotide GTR":{\n-     "AIC-c":7112.857317645923,\n-     "Equilibrium frequencies":      [\n-[0.3592490842490842],\n-      [0.181959706959707],\n-      [0.240018315018315],\n-      [0.2187728937728937] \n-      ],\n-     "Log Likelihood":-3532.321228205235,\n-     "Rate Distributions":{\n-       "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,\n-       "Substitution rate from nucleotide A to nucleotide G":1,\n-       "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,\n-       "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,\n-       "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,\n-       "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399\n-      },\n-     "display order":0,\n-     "estimated parameters":24\n-    }\n-  },\n- "input":{\n-   "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/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)Node3:0.08509899999999999,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-   "P-value threshold":0.05,\n-   "positive test results":0,\n-   "tested":16\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-   "Baseline model fitting":{\n-     "order":2,\n-     "timer":17\n-    },\n-   "Complexity analysis":{\n-     "order":3,\n-     "timer":110\n-    },\n-   "Full adaptive model fitting":{\n-     "order":4,\n-     "timer":20\n-    },\n-   "Overall":{\n-     "order":0,\n-     "timer":259\n-    },\n-   "Preliminary model fitting":{\n-     "order":1,\n-     "timer":0\n-    },\n-   "Testing for selection":{\n-     "order":5,\n-     "timer":112\n-    }\n-  }\n-}\n\\ No newline at end of file\n'
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/absrel-out2.json
--- a/test-data/absrel-out2.json Thu Aug 18 14:02:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,535 +0,0 @@\n-{\n- "Synonymous site-posteriors":  [\n-[0.2237313836650769, 0.07034985497742986, 0.07145045464678079, 0.162904629542773, 0.08696014489632299, 0.4973049561752621, 0.9385366945295869, 0.07695133428552869, 0.001997373788362212, 0.000990883865044414, 1.597366276160643e-05, 0.001639173387605954, 0.0006726936008082838, 0.0005936260958686961, 0.01218331055979857, 6.818341915747173e-05, 3.10538784980663e-05, 0.0003850280284965983, 1.706749658825067e-05, 1.954717668341298e-05, 5.757139486184149e-05, 5.547696233589325e-07, 0.1027014607202221, 0.0005061229953062066, 0.0002713590976491243, 0.01071054750911007, 0.01058998805403938, 0.001824707456373813, 0.1040310240977791, 0.007394679956619656, 0.01548570716335477, 0.0008559908124777675, 0.0001902341284497764, 0.04379131907975038, 0.0001602246750758031, 0.872186620749095, 0.007390732327759301, 0.06674897008912457, 0.06972624550033353, 0.09402374412106476, 0.1105108657459435, 0.01328650075574577, 0.0004656132149530012, 0.02510551997724948, 2.726156324850206e-05, 0.218781542689419, 0.006387422790697847, 0.007440221639665756, 0.05243297879242407, 0.1290026685674839, 0.6362466982390221, 0.8443663408237136, 0.0008463748207276134, 0.07321341035497612, 0.7855063534903601, 0.3150726276771443, 0.8508489144151971, 0.02756928287263707, 0.01299322935453241, 0.01615676639466097, 0.1381872019916541, 0.06580359020038734, 0.007948607169236543, 0.03623393203353259, 0.001127119071510586, 2.510588082439908e-07, 0.001198735279712407, 1.499028692444743e-05, 0.0007376828878749214, 0.0001439329508670455, 0.0003622577009774282, 0.02916632660997443, 0.09212248703639002, 7.45231360132705e-06, 0.2140082858090768, 0.009508570249567472, 0.5162459275326868, 0.001293919095115566, 0.8726414064830788, 0.0001302201041918639, 0.003094500709258363, 0.002116963683292442, 0.001652532423559578, 2.885330472177516e-05, 0.8679630109050446, 0.06064786452319544, 0.01926710656265205, 0.003438784053820811, 0.04592043108186669, 0.009356125116963642, 1.39030344053496e-06, 0.1492915058063837, 0.07707061704057379, 0.07475315743864808, 0.000302419021163877, 0.144336435993247, 0.003223470679335452, 0.03037745915910377, 0.0003011350589031628, 0.006808005110601785, 0.0008232735328502056, 0.03833979319278999, 9.698364220287434e-05, 0.004939487216502053, 6.693653877999158e-05, 0.02813691694081084, 9.485847293237623e-06, 9.213850857247055e-06, 0.0653963700817919, 3.36098340810195e-05, 0.3256932672291724, 4.035388925446032e-05, 0.04374256630355731, 0.0001602246750758031, 0.4014805201846622, 7.992404162601145e-05, 0.01019186788933821, 5.157202070064211e-05, 0.01632615592433439, 2.711206299164022e-05, 1.39112911627399e-05, 0.0001144909315662084, 0.0001470176943661007, 0.008065109594132992, 0.0001053551543690356, 0.09762185907634006, 0.2690693395574275, 2.306365194486018e-06, 0.001629982970373876, 0.0005166683932434172, 0.008811904607316576, 0.004707366984528872, 0.0005329112697905272, 0.004709232000043501, 5.309771784866412e-06, 0.02081799460860159, 0.01482206699240225, 0.02247987076174615, 0.03334725806979871, 0.5823700494422802, 0.6236724985801352, 0.0185646271114748, 0.1682321476102055, 0.5117950109841621, 0.02454309603098215, 0.01143016187387928, 0.03611174379314762, 0.001160042508580727, 0.008675955890656782, 0.0006207030249667641, 0.3189329652004703, 0.009022200481586255, 0.00453169826721376, 0.01175652549884987, 0.03798598471232684, 3.415462094795308e-05, 0.02071616557444895, 0.01314271860208286, 0.2919550074913849, 0.01463675769845591, 0.3808264251791824, 0.0005743039294857045, 0.0001968101730522108, 8.98952537201286e-05, 0.07242504371764499, 0.0003645543853153564, 0.3778182412645538, 6.623577458551056e-06, 0.423433584889663, 6.299717466720515e-06, 0.0002383566395190999, 0.05603244198717539, 0.001549983450584894, 0.002286903228642564, 0.05910553215170956, 0.1696354264894034, 0.008408717444453151, 0.1784153043909985, 0.005750339228228735, 0.1911339411346325, 2.211643409474936e-06, 0.0005399645955134869, 0.00037995024257006'..b'55364640413],\n-      [0.01055038238273567],\n-      [0.01311330258173711],\n-      [0.01100238215235291],\n-      [0.01931219560697892],\n-      [0.0157719705998612],\n-      [0.01960332955558842],\n-      [0.01644767379420349],\n-      [0.01965132601881859],\n-      [0.02049322866376102],\n-      [0.008933621043463411],\n-      [0.007295949736387736],\n-      [0.009068296583349953],\n-      [0.007608523013862737],\n-      [0.007628698224327205],\n-      [0.009481877006094248],\n-      [0.00795552712159237],\n-      [0.01396413011303752],\n-      [0.01140428846505027],\n-      [0.01417464125436193],\n-      [0.01189287130232129] \n-      ],\n-     "Log Likelihood":-3399.656647852504,\n-     "Rate Distributions":{\n-       "Per-branch delta":{\n-         "2.5%":0,\n-         "97.5%":10.66318587577853,\n-         "Mean":1.142287895998736,\n-         "Median":0.2080459069952131\n-        },\n-       "Per-branch omega":{\n-         "2.5%":0,\n-         "97.5%":2.028136557891868,\n-         "Mean":666666667.5178814,\n-         "Median":1\n-        },\n-       "Synonymous site-to-site rates":{\n-         "0":{\n-           "proportion":0.3499070593950995,\n-           "rate":0.3584907731592092\n-          },\n-         "1":{\n-           "proportion":0.5579704535685105,\n-           "rate":1.083607309819905\n-          },\n-         "2":{\n-           "proportion":0.09212248703639001,\n-           "rate":2.93023662601063\n-          }\n-        }\n-      },\n-     "display order":1,\n-     "estimated parameters":67\n-    },\n-   "Full adaptive model":{\n-     "AIC-c":6937.867430345418,\n-     "Log Likelihood":-3399.405413285916,\n-     "Rate Distributions":{\n-      },\n-     "display order":2,\n-     "estimated parameters":67\n-    },\n-   "Nucleotide GTR":{\n-     "AIC-c":7112.857288723968,\n-     "Equilibrium frequencies":      [\n-[0.3592490842490842],\n-      [0.181959706959707],\n-      [0.240018315018315],\n-      [0.2187728937728937] \n-      ],\n-     "Log Likelihood":-3532.321213744258,\n-     "Rate Distributions":{\n-       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,\n-       "Substitution rate from nucleotide A to nucleotide G":1,\n-       "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,\n-       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,\n-       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,\n-       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741\n-      },\n-     "display order":0,\n-     "estimated parameters":24\n-    }\n-  },\n- "input":{\n-   "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",\n-   "number of sequences":10,\n-   "number of sites":187,\n-   "partition count":1,\n-   "trees":{\n-     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n-    }\n-  },\n- "runtime":"2.5.36",\n- "test results":{\n-   "P-value threshold":0.05,\n-   "positive test results":0,\n-   "tested":16\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-   "Baseline model fitting":{\n-     "order":2,\n-     "timer":129\n-    },\n-   "Complexity analysis":{\n-     "order":3,\n-     "timer":406\n-    },\n-   "Full adaptive model fitting":{\n-     "order":4,\n-     "timer":46\n-    },\n-   "Overall":{\n-     "order":0,\n-     "timer":1006\n-    },\n-   "Preliminary model fitting":{\n-     "order":1,\n-     "timer":0\n-    },\n-   "Testing for selection":{\n-     "order":5,\n-     "timer":424\n-    }\n-  }\n-}\n\\ No newline at end of file\n'
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/busted-out1.json
--- a/test-data/busted-out1.json Thu Aug 18 14:02:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,394 +0,0 @@\n-{\n- "Evidence Ratios":{\n-   "constrained":    [\n-[1.751697313438667, 0.9490151622254345, 0.9575938099872893, 1.827482077500528, 1.505094606485015, 2.088346790071941, 7.070051504373732, 3.867967952992799, 2.545750919582881, 0.7247660693488289, 0.3196737937441124, 1.489449650902744, 0.6530151351740718, 1.04337285373284, 1.058333334239147, 0.5088801718500566, 0.8550055907613735, 1.110381942461004, 0.565683766000719, 0.6740763008813015, 0.4649952970969699, 0.4036426325687712, 2.442336342315371, 0.9859501295040206, 1.104892115806872, 1.062417300927637, 1.753888646580218, 1.31233150141181, 1.885518048500539, 0.7894296553774935, 0.723576644239061, 0.8827532839004689, 0.6984548336173313, 4.520258616283331, 0.501963856483453, 1.807812329244406, 0.6240669422720765, 0.9486848826066486, 0.9673516986934556, 1.479968294590536, 1.364799619489093, 1.709865961585205, 1.218557239747954, 0.7108467425303473, 0.3215450048962207, 2.271412336163041, 0.6355183534074139, 0.8839058954441763, 1.497501825835906, 2.637709102972778, 1.711470421506773, 3.027431470913309, 1.57278424917318, 3.277990564747366, 6.926286311855851, 3.784092751645639, 3.146955337815139, 1.955427417762355, 2.022694964562529, 0.666396825353515, 3.560060598929708, 1.666971860419219, 1.738637096007019, 3.220829375167113, 0.3447106216301303, 0.4881402535027675, 1.387141991322175, 0.5556476307196163, 0.6310295884570762, 0.4580705327203016, 0.4272583872429177, 2.901848650844198, 0.9999999999999991, 1.027519028508734, 2.915165037860989, 2.8354880840935, 1.858569677080054, 0.4521292148676688, 3.009136246768449, 0.705314987368983, 2.743480940643173, 0.3932432097494273, 0.9370673501878248, 0.4620247121091633, 2.83829096947346, 0.9007779218604833, 0.3302046680129435, 1.07627096358673, 1.391320542790854, 1.521972158264955, 0.4323783230969274, 2.334048026570822, 2.149795581008433, 3.074008352247498, 0.4499660997382409, 1.699461664815503, 0.8463586773204229, 2.696688856522739, 0.5804226171984278, 1.135876829610681, 0.8103519829402507, 2.896966803514224, 0.8351241901463535, 1.602690102144888, 0.7282588483860968, 2.78698806913424, 0.9149220061406503, 0.6214951247464974, 1.819052515045006, 0.2353728426618933, 2.441495991316177, 0.4689975029575301, 6.36479070098702, 0.501963856483453, 1.155173566804371, 0.3029791752249296, 3.710694239289469, 0.7371667962152887, 1.911346283016054, 0.3691203298834842, 1.027711744192628, 1.502724363578014, 0.3011502503588185, 0.9854850481813123, 0.3756291290353144, 4.112619261559145, 2.95680467264194, 0.4290868700547413, 0.4685206821924932, 0.4059560116267469, 2.50268310954176, 0.5227540827634783, 0.4671119113495291, 0.9338453011500626, 0.5571522059019809, 0.5886144003589358, 1.839204151926823, 1.060599026952742, 3.125234562282934, 2.54439731915596, 5.066889740057174, 2.915048895304102, 1.905524097635808, 2.212264991895895, 3.738815510070657, 2.074128973780481, 3.31083714843465, 0.6408491718084866, 3.068722634962862, 0.9229478196348808, 2.172843296216792, 1.750529904876356, 1.222415748191823, 1.340180507105605, 1.65676234501901, 1.177884311452671, 1.853985207061093, 1.949028686126, 1.848056555892881, 1.490331787720329, 2.808897643683787, 0.5370047325763545, 0.754447735175597, 0.292920631250886, 1.922199953975427, 0.2194780669088011, 2.411432550287456, 0.4936742969382611, 2.687417056073211, 0.8937719293629136, 0.630203462304753, 3.500554848762429, 0.8047116371904648, 2.9258711565943, 2.978602987543041, 1.892870394871532, 1.224886235480212, 3.334368853761007, 1.443700495825233, 1.7051887541283, 0.480593393899601, 0.907604501104216, 0.9198540076829841, 0.8702783448030316, 0.4699917745647508, 0.6213048344098008, 0.9960464828596589] \n-    ],\n-   "optimized null":    [\n-[1.115754847329475, 0.9981043798375602, 0.9996678649277134, 1.027524895296611, 0.7950614097315224, 0.6815044886735678, 0.9660630441693723, 1.768207537367336, 1.995453831253169, 0.9376497008654193, 0.6553491413144868, 1.461081981960806, 1.013114798606584, 1.166859848568389, 0.60149018717580'..b'3156],\n-      [0.01052248035033209],\n-      [0.01291855364640413],\n-      [0.01055038238273567],\n-      [0.01311330258173711],\n-      [0.01100238215235291],\n-      [0.01931219560697892],\n-      [0.0157719705998612],\n-      [0.01960332955558842],\n-      [0.01644767379420349],\n-      [0.01965132601881859],\n-      [0.02049322866376102],\n-      [0.008933621043463411],\n-      [0.007295949736387736],\n-      [0.009068296583349953],\n-      [0.007608523013862737],\n-      [0.007628698224327205],\n-      [0.009481877006094248],\n-      [0.00795552712159237],\n-      [0.01396413011303752],\n-      [0.01140428846505027],\n-      [0.01417464125436193],\n-      [0.01189287130232129] \n-      ],\n-     "Log Likelihood":-3467.012706765863,\n-     "Rate Distributions":{\n-       "non-synonymous/synonymous rate ratio for *test*":        [\n-[0.9959842858928788, 1] \n-        ]\n-      },\n-     "display order":1,\n-     "estimated parameters":31\n-    },\n-   "Nucleotide GTR":{\n-     "AIC-c":7112.857310169033,\n-     "Equilibrium frequencies":      [\n-[0.3592490842490842],\n-      [0.181959706959707],\n-      [0.240018315018315],\n-      [0.2187728937728937] \n-      ],\n-     "Log Likelihood":-3532.32122446679,\n-     "Rate Distributions":{\n-       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,\n-       "Substitution rate from nucleotide A to nucleotide G":1,\n-       "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,\n-       "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,\n-       "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,\n-       "Substitution rate from nucleotide G to nucleotide T":0.304509117524575\n-      },\n-     "display order":0,\n-     "estimated parameters":24\n-    },\n-   "Unconstrained model":{\n-     "AIC-c":6910.776988890891,\n-     "Log Likelihood":-3414.491829601268,\n-     "Rate Distributions":{\n-       "Synonymous site-to-site rates":{\n-         "0":{\n-           "proportion":0.2655037162058198,\n-           "rate":0.2749303122566129\n-          },\n-         "1":{\n-           "proportion":0.6321791898264187,\n-           "rate":0.9740711294478059\n-          },\n-         "2":{\n-           "proportion":0.1023170939677615,\n-           "rate":3.041695877803997\n-          }\n-        },\n-       "Test":{\n-         "0":{\n-           "omega":0,\n-           "proportion":0.386646389823596\n-          },\n-         "1":{\n-           "omega":0.9964438830494696,\n-           "proportion":0\n-          },\n-         "2":{\n-           "omega":1.876622752045829,\n-           "proportion":0.613353610176404\n-          }\n-        }\n-      },\n-     "display order":2,\n-     "estimated parameters":40\n-    }\n-  },\n- "input":{\n-   "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta",\n-   "number of sequences":10,\n-   "number of sites":187,\n-   "partition count":1,\n-   "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":10.17667489929045,\n-   "p-value":0.003084133210483175\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":70\n-    },\n-   "Overall":{\n-     "order":0,\n-     "timer":451\n-    },\n-   "Preliminary model fitting":{\n-     "order":1,\n-     "timer":10\n-    },\n-   "Unconstrained BUSTED model fitting":{\n-     "order":2,\n-     "timer":370\n-    }\n-  }\n-}\n\\ No newline at end of file\n'
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/busted-out2-1.json
--- a/test-data/busted-out2-1.json Thu Aug 18 14:02:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,369 +0,0 @@\n-{\n- "Evidence Ratios":{\n-   "constrained":    [\n-[0.9923402064246108, 0.9931062434543886, 0.9924143522123878, 0.9923806778416975, 0.9931062434543886, 0.9931472643200557, 0.9926477905890503, 0.9927770719239265, 0.9925333152392071, 0.9927770719239265, 0.9934702178721884, 0.9943672356427694, 0.9934310695695089, 0.9925333152392071, 0.9924430461178078, 0.9926389443188771, 0.9929336452766124, 0.992205754049072, 0.9925333152392071, 0.9934702178721884, 0.9928933056224403, 0.9934702178721884, 0.9932730568068178, 0.9932283919959691, 0.992533339256682, 0.9942200873476073, 0.9925611908926516, 0.9931448487922603, 0.9939853880387395, 0.9934702178721884, 0.99293384770743, 0.9934702178721884, 0.9925179551267049, 0.9943679446048819, 0.9927773049889533, 0.9931443273636676, 0.9931062434543886, 0.9925134341549778, 0.9925611909005787, 0.9931473014288434, 0.9926389443198911, 0.9931443273636676, 0.9934310695695089, 0.9931443273636676, 0.9924780389922671, 0.9934702178721884, 0.9931062434543886, 0.9932804150557601, 0.9934726274784342, 0.9931062434543886, 0.9924219863349872, 0.9923806778416975, 0.9931443273636676, 0.9931435821987634, 0.9925333152392071, 0.9936257920351428, 0.9931435821376157, 0.9926477905890503, 0.9925333152392071, 0.9927779069991203, 0.9929437554492885, 0.9925017439584489, 0.99293384770743, 0.9934310695695089, 0.9934702178721884, 0.9934721013907659, 0.9924251009388676, 0.9924141340632909, 0.9926477905495983, 0.9934711740617125, 0.9932283919959691, 0.9925177139913511, 0.9934702178721884, 0.9943672356427694, 0.9927770719239265, 0.9929336452766124, 0.9925197420367843, 0.9925177139913511, 0.9931443273636676, 0.9925105155914694, 0.9931435821376157, 0.9934310695695089, 0.9925183863200961, 0.9926477905890503, 0.9932730568068178, 0.9924251010701199, 0.9925197420424023, 0.9932283919959691, 0.9931443296040251, 0.9928933176006907, 0.993273371715983, 0.9943672378832206, 0.9924430473679494, 0.99293384770743, 0.9925333184105342, 0.9926630435645116, 0.9923809642370167, 5.534127900729341, 0.9924219864121104, 0.9943682197206795, 0.9934702311259231, 0.9934310695695089, 0.9934760025373545, 0.9934702311259231, 0.9932802114960739, 0.9927770729322174, 0.9925611908926516, 0.9927770719239265, 0.9927327100858865, 0.9929336452766124, 0.9925001632546028, 0.9923722834456535, 0.9929336453222932, 0.9925179551267049, 0.9936341873975495, 0.9929437555014818, 0.9932802114960739, 0.9937315476278487, 0.992340204253054, 0.9943672356427694, 0.9929336468714807, 0.9938370469336766, 0.9924251183061013, 0.9925197839911024, 0.9924888069008881, 0.9934342191574459, 0.9936253008137887, 0.9926477893954572, 0.9925179551643614, 0.9929437555006061, 0.9925533562870937, 0.99293384770743, 0.9923806778419063, 0.9924141340632909, 0.9929338477385575, 0.9924723646193916, 0.9931435821376157, 0.9939625941543071, 0.9925611908926516, 0.9925333152392071, 0.9924220612506358, 0.9931062434543886, 0.9925183208373158, 0.9936341873975495, 0.9930060593676604, 0.9933595398184349, 0.9931435821376157, 0.992500165533227, 0.9925105155937887, 0.9925334716346541, 0.9930061381944508, 0.9924431316500499, 0.9932283919959691, 0.9934702178721884, 0.9924430459213518, 0.9932802114960739, 0.9925333184105342, 0.9925179551267049, 0.99293384770743, 0.9925197420367843, 0.9932730568068178, 0.9924141340632909, 0.9922655287420374, 0.9926389443188771, 0.9925611915170334, 0.9934702178721884, 1.003815974390525, 0.9943672356427694, 0.9931242168810309, 0.9923806781609613, 0.9929437554492885, 0.9925180203827441, 0.9934702178721884, 0.9932730568068178, 0.9931435821376157, 0.9925333152392071, 0.9924628213793587, 0.9929339147938504, 0.9928952725654127, 0.9928135530250399, 0.9936341873975495, 0.9932730568068178, 0.9933595398184349, 0.9926389443188771, 0.9929336452766124, 0.9929336452766124, 0.9942200873476073, 0.9936341873975495, 0.9927770719239265, 0.9924430459213518, 0.9926201559100486, 0.9924252056384386, 0.9943672356427694, 0.993145576241621, 0.99293384770743, 0.9924219864121104, 0.9930060593676604, 0.99266304'..b'     [0.008731154380523415],\n-      [0.00884808446536876],\n-      [0.034087812394816],\n-      [0.006527245376826684],\n-      [0.01318932435908579],\n-      [0.01336595951511979],\n-      [0.01178447449308153],\n-      [0.02413128354890585],\n-      [0.0262916585104385],\n-      [0.005034412430862358],\n-      [0.01017282094890981],\n-      [0.01030905823951665],\n-      [0.004328407393735399],\n-      [0.008746226896405704],\n-      [0.008863358836639712],\n-      [0.03414665788893068],\n-      [0.006538513303760755],\n-      [0.0132120929750345],\n-      [0.01338903305480236] \n-      ],\n-     "Log Likelihood":-3175.995949441886,\n-     "Rate Distributions":{\n-       "non-synonymous/synonymous rate ratio for *background*":        [\n-[0.2379324068936849, 1] \n-        ],\n-       "non-synonymous/synonymous rate ratio for *test*":        [\n-[0.1777604776475358, 1] \n-        ]\n-      },\n-     "display order":1,\n-     "estimated parameters":29\n-    },\n-   "Nucleotide GTR":{\n-     "AIC-c":6683.094244259512,\n-     "Equilibrium frequencies":      [\n-[0.4044507575757576],\n-      [0.1662878787878788],\n-      [0.2095643939393939],\n-      [0.2196969696969697] \n-      ],\n-     "Log Likelihood":-3320.503280793639,\n-     "Rate Distributions":{\n-       "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,\n-       "Substitution rate from nucleotide A to nucleotide G":1,\n-       "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,\n-       "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,\n-       "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,\n-       "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568\n-      },\n-     "display order":0,\n-     "estimated parameters":21\n-    },\n-   "Unconstrained model":{\n-     "AIC-c":6400.149223170942,\n-     "Log Likelihood":-3162.670820660715,\n-     "Rate Distributions":{\n-       "Background":{\n-         "0":{\n-           "omega":0.1679188282558003,\n-           "proportion":0.8207520434237199\n-          },\n-         "1":{\n-           "omega":0.2120937673953722,\n-           "proportion":0.1693698006934513\n-          },\n-         "2":{\n-           "omega":13.84252711122189,\n-           "proportion":0.00987815588282877\n-          }\n-        },\n-       "Test":{\n-         "0":{\n-           "omega":0.08367159828032572,\n-           "proportion":0.9533274940567786\n-          },\n-         "1":{\n-           "omega":0.2493792697064242,\n-           "proportion":0.03716922067476962\n-          },\n-         "2":{\n-           "omega":34.20463703717275,\n-           "proportion":0.009503285268451747\n-          }\n-        }\n-      },\n-     "display order":2,\n-     "estimated parameters":37\n-    }\n-  },\n- "input":{\n-   "file name":"/tmp/tmpfzf3u9m4/job_working_directory/000/2/working/./input.nex",\n-   "number of sequences":8,\n-   "number of sites":440,\n-   "partition count":1,\n-   "trees":{\n-     "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"\n-    }\n-  },\n- "test results":{\n-   "LRT":3.465106677611402,\n-   "p-value":0.08841616008911996\n-  },\n- "tested":{\n-   "0":{\n-     "B_FR_83_HXB2":"background",\n-     "B_US_83_RF":"background",\n-     "B_US_86_JRFL":"background",\n-     "B_US_90_WEAU160":"test",\n-     "D_CD_83_ELI":"background",\n-     "D_CD_83_NDK":"background",\n-     "D_CD_84_84ZR085":"background",\n-     "D_UG_94_94UG114":"background",\n-     "Node1":"background",\n-     "Node10":"background",\n-     "Node2":"background",\n-     "Node3":"background",\n-     "Node9":"background"\n-    }\n-  },\n- "timers":{\n-   "Constrained BUSTED model fitting":{\n-     "order":3,\n-     "timer":14\n-    },\n-   "Overall":{\n-     "order":0,\n-     "timer":60\n-    },\n-   "Preliminary model fitting":{\n-     "order":1,\n-     "timer":3\n-    },\n-   "Unconstrained BUSTED model fitting":{\n-     "order":2,\n-     "timer":40\n-    }\n-  }\n-}\n\\ No newline at end of file\n'
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/busted-out2-2.json
--- a/test-data/busted-out2-2.json Thu Aug 18 14:02:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b"@@ -1,3395 +0,0 @@\n-#NEXUS\n-\n-BEGIN TAXA;\n-\tDIMENSIONS NTAX = 8;\n-\tTAXLABELS\n-\t\t'B_FR_83_HXB2' 'B_US_83_RF' 'B_US_86_JRFL' 'B_US_90_WEAU160' 'D_CD_83_ELI' 'D_CD_83_NDK' 'D_CD_84_84ZR085' 'D_UG_94_94UG114' ;\n-END;\n-\n-BEGIN CHARACTERS;\n-\tDIMENSIONS NCHAR = 1320;\n-\tFORMAT\n-\t\tDATATYPE = DNA\n-\t\tGAP=-\n-\t\tMISSING=?\n-\t;\n-\n-MATRIX\n-\t'B_FR_83_HXB2'    CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC\n-\t'B_US_83_RF'      CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCATTGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCACAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAATCTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACCGGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAGCTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCATAATAGGAGCAGAAACTTTC\n-\t'B_US_86_JRFL'    CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCGCAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCAAAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGTGTATTATGACCCATCAAAAGACT"..b'6503784977386*t*busted.test.theta_AT*busted.test.omega3;\n-busted.test_Q_component_3[60][53]:=0.1818409092376876*t*busted.test.theta_CT*busted.test.omega3;\n-busted.test_Q_component_3[60][56]:=0.1563402972714242*t*busted.test.theta_GT*busted.test.omega3;\n-busted.test_Q_component_3[60][57]:=0.5074830879161225*t*busted.test.theta_AT*busted.test.omega3;\n-busted.test_Q_component_3[60][58]:=0.09717451507454297*t*busted.test.theta_CT;\n-busted.test_Q_component_3[60][59]:=0.1963563685387479*t*busted.test.theta_GT*busted.test.omega3;\n-\n-\n-busted.test_pi={\n-{0.07535940345366139} \n-{0.01443006409728228} \n-{0.02915821068672351} \n-{0.02954870567752823} \n-{0.03219408024958758} \n-{0.006164627375802654} \n-{0.01245659774045292} \n-{0.01262342001471309} \n-{0.0276793164843978} \n-{0.005300125700761717} \n-{0.01070973633984303} \n-{0.01085316415297191} \n-{0.0418125103783387} \n-{0.008006395714089126} \n-{0.01617817990958604} \n-{0.0163948426631036} \n-{0.0409913146415633} \n-{0.007849150478922548} \n-{0.01586044121725868} \n-{0.01607284872448998} \n-{0.01751178502783737} \n-{0.003353213651232053} \n-{0.006775694789785172} \n-{0.006866436807635995} \n-{0.01505600521072376} \n-{0.002882972930821469} \n-{0.005825499564956559} \n-{0.005903516300053625} \n-{0.02274367484777162} \n-{0.004355032959661065} \n-{0.008800028033786655} \n-{0.008917880494044083} \n-{0.06143704799998004} \n-{0.01176416611541591} \n-{0.0237713451467977} \n-{0.0240896977132239} \n-{0.0262463496652457} \n-{0.005025736545566795} \n-{0.01015528996016046} \n-{0.01029129247081581} \n-{0.02256567087217255} \n-{0.004320948178469224} \n-{0.008731154380523415} \n-{0.00884808446536876} \n-{0.034087812394816} \n-{0.006527245376826684} \n-{0.01318932435908579} \n-{0.01336595951511979} \n-{0.01178447449308153} \n-{0.02413128354890585} \n-{0.0262916585104385} \n-{0.005034412430862358} \n-{0.01017282094890981} \n-{0.01030905823951665} \n-{0.004328407393735399} \n-{0.008746226896405704} \n-{0.008863358836639712} \n-{0.03414665788893068} \n-{0.006538513303760755} \n-{0.0132120929750345} \n-{0.01338903305480236} \n-};\n-Model busted.test=(\'Exp(busted.test_Q_component_1)*1*busted.test.bsrel_mixture_aux_0+Exp(busted.test_Q_component_2)*1*(1-busted.test.bsrel_mixture_aux_0)*busted.test.bsrel_mixture_aux_1+Exp(busted.test_Q_component_3)*1*(1-busted.test.bsrel_mixture_aux_0)*(1-busted.test.bsrel_mixture_aux_1)\',busted.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n-TRY_NUMERIC_SEQUENCE_MATCH=0;\n-ACCEPT_ROOTED_TREES=0;\n-Tree QCdustmY.tree_id_0=((((D_CD_83_ELI{busted.background},D_CD_83_NDK{busted.background})Node3{busted.background},D_UG_94_94UG114{busted.background})Node2{busted.background},D_CD_84_84ZR085{busted.background})Node1{busted.background},B_US_83_RF{busted.background},((B_FR_83_HXB2{busted.background},B_US_86_JRFL{busted.background})Node10{busted.background},B_US_90_WEAU160{busted.test})Node9{busted.background});\n-\n-QCdustmY.tree_id_0.D_CD_83_ELI.t=0.1370833707498818;\n-QCdustmY.tree_id_0.D_CD_83_NDK.t=0.06548157292895862;\n-QCdustmY.tree_id_0.Node3.t=0.08713663976914707;\n-QCdustmY.tree_id_0.D_UG_94_94UG114.t=0.4280587759297035;\n-QCdustmY.tree_id_0.Node2.t=0.01513176299488742;\n-QCdustmY.tree_id_0.D_CD_84_84ZR085.t=0.2130038858362291;\n-QCdustmY.tree_id_0.Node1.t=0.1846586758901705;\n-QCdustmY.tree_id_0.B_US_83_RF.t=0.2063734346567031;\n-QCdustmY.tree_id_0.B_FR_83_HXB2.t=0.08448292129897501;\n-QCdustmY.tree_id_0.B_US_86_JRFL.t=0.1299787017728399;\n-QCdustmY.tree_id_0.Node10.t=0.01154139173279806;\n-QCdustmY.tree_id_0.B_US_90_WEAU160.t=0.1759147205880889;\n-QCdustmY.tree_id_0.Node9.t=0.03592645553508322;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n-SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n-\n-DataSet busted.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n-DataSetFilter busted.filter.default = CreateFilter(busted.codon_data,3,"0-1319","4,5,7,6,1,0,2,3","TAA,TAG,TGA");\n-ASSUME_REVERSIBLE_MODELS=1;\n-USE_LAST_RESULTS=0;\n-LikelihoodFunction QCdustmY.likelihoodFunction = (busted.filter.default,QCdustmY.tree_id_0);\n-\n-END;\n\\ No newline at end of file\n'
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/conv-out1.nex
--- a/test-data/conv-out1.nex Thu Aug 18 14:02:04 2022 +0000
+++ b/test-data/conv-out1.nex Thu Mar 02 15:10:54 2023 +0000
b
b'@@ -16,8 +16,8 @@\n \t;\n \n MATRIX\n- ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ET\n- ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????\n+ -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ET\n+ -----------------------------------------------------------------------------------------------------------------------------------------'..b'--------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n  LVFFFVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGLSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDLSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n  MYVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPVTVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n  MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n'
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/relax-in1.nhx
--- a/test-data/relax-in1.nhx Thu Aug 18 14:02:04 2022 +0000
+++ b/test-data/relax-in1.nhx Thu Mar 02 15:10:54 2023 +0000
b
@@ -1,1 +1,1 @@
-(((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Baboon:0.011873):0.340802,Rat:0.050958)
+(((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Baboon:0.011873):0.340802,Rat:0.050958);
b
diff -r 6761212b7f1d -r beeeed9665ea test-data/slac-out1.json
--- a/test-data/slac-out1.json Thu Aug 18 14:02:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,2076 +0,0 @@\n-{\n- "MLE":{\n-   "content":{\n-     "0":{\n-       "by-branch":{\n-         "AVERAGED":          [\n-[131.3409038539508, 387.3032052553191, 18.83333333333334, 62.16666666666666, 0.2532389774551154, 0.1433927495601502, 0.1605116245440958, 0.009922319377965909, 0.3896479078188506, 0.7050801922163503, 0.190671339253091],\n-          [129.582341679606, 390.2657462377136, 20.16666666666666, 84.83333333333334, 0.2492696322088151, 0.1556282006118473, 0.2173732492568301, 0.03578822166983051, 0.1057124571474986, 0.9315947329811959, 0.2526189686412594],\n-          [133.5634277511288, 389.0892183853288, 9, 31, 0.255549127586847, 0.06738371537431539, 0.07967324339812369, 0.007123167975176309, 0.4078805639677862, 0.7273413969784412, 0.100661445687484],\n-          [136.3001744404261, 388.2752414674823, 20.66666666666666, 73.33333333333334, 0.2598295122247097, 0.1516261204471138, 0.1888694552250377, 0.02158671423873519, 0.2256328450945964, 0.8402434326037131, 0.2128981270938909],\n-          [133.8191805302023, 389.2442828476442, 23, 92, 0.2558373694580443, 0.1718737172718601, 0.2363554303917937, 0.03737442747928117, 0.1006659765808149, 0.9336498751512877, 0.270986057489719],\n-          [140.2315863698817, 396.7622548627548, 7.5, 18.5, 0.2611418895382275, 0.05348295768556476, 0.0466274192498462, -0.003973557954650256, 0.7090493474259939, 0.4503697460596697, 0.0674227399326417],\n-          [134.7817325168444, 392.4918226549124, 0, 3, 0.2556201258243265, 0, 0.007643471345994557, 0.004430253969516925, 0.4124619282373314, 1, 0.003845100000905624],\n-          [136.1184811420076, 397.1417020142569, 1, 0, 0.255257162341183, 0.007346540981137861, 0, -0.004258149323861931, 1, 0.255257162341183, 0.001710698008755675],\n-          [136.5467837843545, 396.817130340981, 6, 8, 0.2560105402111387, 0.04394098369593, 0.02016041997260975, -0.01378351956376455, 0.9568131059753749, 0.1225532921657104, 0.0261290773391622],\n-          [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n-          [136.6003799486803, 396.6078513587676, 0, 1, 0.2561858049597822, 0, 0.002521382258505542, 0.001461425477216891, 0.7438141950402177, 1, 0.001852173963769908],\n-          [136.9415154360939, 396.3923665097976, 4.5, 4.5, 0.2567650773216525, 0.03286074340326692, 0.01135238813911109, -0.01246651841466516, 0.9670681040365207, 0.116490042971819, 0.01816964082591924],\n-          [138.8593313638795, 397.772580198107, 9, 39, 0.2587608533374368, 0.06481379329427697, 0.09804597385917452, 0.01926179784012569, 0.1682548120106906, 0.905709700565171, 0.1081901197733327],\n-          [143.8068579584112, 396.4414008640307, 42.50000000000001, 70.5, 0.2661866199659049, 0.295535279772895, 0.1778320827399651, -0.06822228177164953, 0.9959804586708396, 0.007098480560500553, 0.28199060274564],\n-          [145.8733144714348, 394.7876057082412, 10, 23, 0.2698055454478885, 0.06855263442963876, 0.05825917447113987, -0.005966221338044341, 0.7401529271181795, 0.3966272436071658, 0.06785010407729926],\n-          [145.261732918168, 395.7720178098857, 21, 35, 0.2684892258989267, 0.1445666355352526, 0.08843475138460322, -0.03253475957690278, 0.9711633315400029, 0.05307382915791914, 0.1202934609265267] \n-          ],\n-         "NAMES":          [\n-["Pig"],\n-          ["Cow"],\n-          ["Node3"],\n-          ["Horse"],\n-          ["Cat"],\n-          ["Node2"],\n-          ["RhMonkey"],\n-          ["Baboon"],\n-          ["Node9"],\n-          ["Human"],\n-          ["Chimp"],\n-          ["Node12"],\n-          ["Node8"],\n-          ["Node1"],\n-          ["Rat"],\n-          ["Mouse"] \n-          ],\n-         "RESOLVED":          [\n-[131.3409038539508, 387.3032052553191, 18.83333333333334, 62.16666666666666, 0.2532389774551154, 0.1433927495601502, 0.1605116245440958, 0.009922319377965909, 0.3896479078188506, 0.7050801922163503, 0.190671339253091],\n-          [129.582341679606, 390.2657462377136, 20.16666666666666, 84.83333333333334, 0.2492696322088151, 0.1556282006118473, 0.2173732492568301, 0.035788221669'..b'0, 0, 0.1387249812240129, 0, 0, 0, 1, 1, 1.725289655759397],\n-      [0.6659596192381536, 2.256767693355746, 2.5, 6, 0.2284450217013008, 3.443359136114996, 2.639155331188279, -0.367350344747201, 0.7673619164483392, 0.5300792745888832, 1.725289655759397],\n-      [1, 2, 0, 1, 0.3333333333333333, 0, 0.4999999999999999, 0.2898064092199763, 0.6666666666666667, 1, 1.725289655759397],\n-      [0.459387925258634, 2.540612074741366, 1, 2, 0.1531293084195447, 2.176809500243183, 0.7872118769661439, -0.8054285949250646, 0.9368355759475115, 0.3926328355868177, 1.725289655759397],\n-      [0.68260572574677, 2.182710391950513, 0, 5.416666666666666, 0.238230511995077, 0, 2.477393204043783, 1.327736424808056, 0.2565180128752361, 1, 1.725289655759397],\n-      [0.6209312921230391, 2.230235398735714, 1, 2, 0.2177814766543932, 1.610484143230854, 0.8967663239197839, -0.4136799968217064, 0.8783719010971742, 0.5213872231511146, 1.725289655759397],\n-      [0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