annotate test-data/fel-out1.json @ 3:c046f72e5e3a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"

{
 "analysis":{
   "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    ",
   "version":"2.00",
   "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",
   "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
   "contact":"[e-mail]",
   "requirements":"in-frame codon alignment and a phylogenetic tree"
  },
 "input":{
   "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta",
   "number of sequences":10,
   "number of sites":187,
   "partition count":1,
   "trees":{
     "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)"
    }
  },
 "fits":{
   "Nucleotide GTR":{
     "Log Likelihood":-3531.963798530155,
     "estimated parameters":24,
     "AIC-c":7112.142458295762,
     "Equilibrium frequencies":[
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      [0.1837789661319073],
      [0.2402852049910873],
      [0.2196078431372549]
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     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,
       "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
       "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
       "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
      },
     "display order":0
    },
   "Global MG94xREV":{
     "Log Likelihood":-3466.725508616141,
     "estimated parameters":31,
     "AIC-c":6996.530451399855,
     "Equilibrium frequencies":[
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     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":[
        [0.9970623081401093, 1]
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     "display order":1
    }
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 "timers":{
   "Total time":{
     "timer":240,
     "order":0
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   "Model fitting":{
     "timer":21,
     "order":1
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   "FEL analysis":{
     "timer":208,
     "order":2
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 "tested":{
   "0":{
     "Pig":"test",
     "Cow":"test",
     "Node3":"test",
     "Horse":"test",
     "Cat":"test",
     "Node2":"test",
     "RhMonkey":"test",
     "Baboon":"test",
     "Node9":"test",
     "Human":"test",
     "Chimp":"test",
     "Node12":"test",
     "Node8":"test",
     "Node1":"test",
     "Rat":"test",
     "Mouse":"test"
    }
  },
 "data partitions":{
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     "name":"fel.filter.default",
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       "original name":"Human",
       "Nucleotide GTR":0,
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    ["beta", "Non-synonymous substitution rate at a site"],
    ["alpha=beta", "The rate estimate under the neutral model"],
    ["LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"],
    ["p-value", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
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