view test-data/absrel-out2.json @ 34:a6619171428e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 14:05:48 +0000
parents 212c958f6cee
children
line wrap: on
line source

{
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 "analysis":{
   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
   "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. v2.3 adds support for SRV",
   "contact":"spond@temple.edu",
   "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.",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"2.3"
  },
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       "Nucleotide GTR":0,
       "Rate Distributions":        [
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       "Uncorrected P-value":1,
       "original name":"Human",
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       "rate at which 2 nucleotides are changed instantly within a single codon":0.2354207827705045
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       "Full adaptive model (synonymous subs/site)":0.01400929685896962,
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       "rate at which 2 nucleotides are changed instantly within a single codon":0
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       "Baseline MG94xREV omega ratio":1.283370430439691,
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       "Full adaptive model":0.2181331361104026,
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       "original name":"Pig",
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       "Baseline MG94xREV omega ratio":0.9234518387715737,
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       "Full adaptive model (non-synonymous subs/site)":0.04934287026354431,
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       "Rate Distributions":        [
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       "Uncorrected P-value":1,
       "original name":"Rat",
       "rate at which 2 nucleotides are changed instantly within a single codon":0.02234985038534893
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       "Full adaptive model":0.003691831254195047,
       "Full adaptive model (non-synonymous subs/site)":0.003691831254195047,
       "Full adaptive model (synonymous subs/site)":1e-10,
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       "Nucleotide GTR":0.003778804730491441,
       "Rate Distributions":        [
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       "Rate classes":1,
       "Uncorrected P-value":0.2385766813428075,
       "original name":"RhMonkey",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
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    },
   "attributes":{
     "Baseline MG94xREV":{
       "attribute type":"branch length",
       "display order":1
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     "Baseline MG94xREV omega ratio":{
       "attribute type":"branch label",
       "display order":1
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     "Corrected P-value":{
       "attribute type":"branch label",
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     "Full adaptive model":{
       "attribute type":"branch length",
       "display order":2
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     "Full adaptive model (non-synonymous subs/site)":{
       "attribute type":"branch label",
       "display order":10
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     "Full adaptive model (synonymous subs/site)":{
       "attribute type":"branch label",
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     "LRT":{
       "attribute type":"branch label",
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     "Nucleotide GTR":{
       "attribute type":"branch length",
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     "Rate Distributions":{
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     "Rate classes":{
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     "Uncorrected P-value":{
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     "original name":{
       "attribute type":"node label",
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      },
     "rate at which 2 nucleotides are changed instantly within a single codon":{
       "attribute type":"branch label",
       "display order":7
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    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
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      ],
     "name":"absrel.filter.default"
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 "fits":{
   "Baseline MG94xREV":{
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     "Equilibrium frequencies":      [
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     "Log Likelihood":-3399.656647852504,
     "Rate Distributions":{
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       "Synonymous site-to-site rates":{
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     "estimated parameters":67
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   "Full adaptive model":{
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     "Log Likelihood":-3399.405413285916,
     "Rate Distributions":{
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     "display order":2,
     "estimated parameters":67
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   "Nucleotide GTR":{
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     "Equilibrium frequencies":      [
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     "Log Likelihood":-3532.321213744258,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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     "display order":0,
     "estimated parameters":24
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 "input":{
   "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",
   "number of sequences":10,
   "number of sites":187,
   "partition count":1,
   "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)"
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 "runtime":"2.5.36",
 "test results":{
   "P-value threshold":0.05,
   "positive test results":0,
   "tested":16
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 "tested":{
   "0":{
     "Baboon":"test",
     "Cat":"test",
     "Chimp":"test",
     "Cow":"test",
     "Horse":"test",
     "Human":"test",
     "Mouse":"test",
     "Node1":"test",
     "Node12":"test",
     "Node2":"test",
     "Node3":"test",
     "Node8":"test",
     "Node9":"test",
     "Pig":"test",
     "Rat":"test",
     "RhMonkey":"test"
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  },
 "timers":{
   "Baseline model fitting":{
     "order":2,
     "timer":129
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   "Complexity analysis":{
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     "timer":406
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   "Full adaptive model fitting":{
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     "timer":46
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   "Overall":{
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     "timer":1006
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   "Preliminary model fitting":{
     "order":1,
     "timer":0
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   "Testing for selection":{
     "order":5,
     "timer":424
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  }
}