annotate test-data/relax-out2-1.json @ 26:9d83d1ab0330 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954

{
 "analysis":0,
 "branch attributes":{
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       "MG94xREV with separate rates for branch sets":0.248802707042435,
       "Nucleotide GTR":0.2480198736772598,
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       "General descriptive":0.3501950875747647,
       "MG94xREV with separate rates for branch sets":0.2891531817656844,
       "Nucleotide GTR":0.2767105173979571,
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       "General descriptive":0.01767952779767795,
       "MG94xREV with separate rates for branch sets":0.0175770110347634,
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       "General descriptive":0.05770620828101171,
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       "General descriptive":0.1330354609631224,
       "MG94xREV with separate rates for branch sets":0.1003154990002797,
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       "General descriptive":0.140369727816558,
       "MG94xREV with separate rates for branch sets":0.1127066220459272,
       "Nucleotide GTR":0.1062201244057951,
       "RELAX alternative":0.1280322211601967,
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       "RELAX partitioned descriptive":0.1406663540457613,
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       "General descriptive":0.02663291940160552,
       "MG94xREV with separate rates for branch sets":0.02627402966233569,
       "Nucleotide GTR":0.02567813733543303,
       "RELAX alternative":0.02720907734174326,
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       "MG94xREV with separate rates for branch sets":0.1921302603267553,
       "Nucleotide GTR":0.1871390433004313,
       "RELAX alternative":0.2174541263946326,
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       "MG94xREV with separate rates for branch sets":0.06831927364558048,
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       "MG94xREV with separate rates for branch sets":0.003755247927570558,
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   "attributes":{
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       "attribute type":"branch length",
       "display order":4
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     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
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     "Nucleotide GTR":{
       "attribute type":"branch length",
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     "RELAX partitioned descriptive":{
       "attribute type":"branch length",
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     "k (general descriptive)":{
       "attribute type":"branch label",
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     "original name":{
       "attribute type":"node label",
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 "data partitions":{
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     "coverage":      [
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      ],
     "name":"relax.filter.default"
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 "fits":{
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     "AIC-c":6945.887251511141,
     "Log Likelihood":-3420.484879880983,
     "Rate Distributions":{
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         "0":{
           "omega":2.201644423775106e-18,
           "proportion":0.1667516969215508
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   "MG94xREV with separate rates for branch sets":{
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     "Equilibrium frequencies":      [
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      [0.0494959405650269],
      [0.04152830682371345],
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      [0.01478480742075003],
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      [0.01140428846505027],
      [0.01417464125436193],
      [0.01189287130232129] 
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     "Log Likelihood":-3461.064187903018,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *Reference*":        [
[1.243401858007084, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *Test*":        [
[0.5612874934764923, 1] 
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     "display order":1,
     "estimated parameters":32
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   "Nucleotide GTR":{
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     "Equilibrium frequencies":      [
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      [0.240018315018315],
      [0.2187728937728937] 
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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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     "estimated parameters":24
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     "Log Likelihood":-3432.482965101608,
     "Rate Distributions":{
       "Reference":{
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           "proportion":0.2968543549269862
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           "proportion":0.2447083724876047
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       "Test":{
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           "proportion":0.2968543549269862
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         "1":{
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           "proportion":0.2447083724876047
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           "proportion":0.4584372725854091
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     "display order":2,
     "estimated parameters":36
    },
   "RELAX null":{
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     "Log Likelihood":-3437.336050862336,
     "Rate Distributions":{
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           "omega":0.07516343499603452,
           "proportion":0.2524283429126023
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         "1":{
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           "proportion":0.3734402861071174
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       "Test":{
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         "1":{
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     "estimated parameters":35
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   "RELAX partitioned descriptive":{
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     "Log Likelihood":-3431.356991882183,
     "Rate Distributions":{
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           "proportion":0.3694476627871225
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         "1":{
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           "proportion":0.1726741298596992
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       "Test":{
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         "1":{
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           "proportion":0.5325206774143161
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           "proportion":0.172106070157943
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     "display order":5,
     "estimated parameters":40
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 "input":{
   "file name":"/tmp/tmps1cqwvdh/job_working_directory/000/5/working/./input.nex",
   "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":{
   "LRT":9.706171521456781,
   "p-value":0.001836502097725456,
   "relaxation or intensification parameter":0.3695692925647034
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 "tested":{
   "0":{
     "BABOON":"Test",
     "CAT":"Reference",
     "CHIMP":"Test",
     "COW":"Reference",
     "HORSE":"Reference",
     "HUMAN":"Test",
     "MOUSE":"Reference",
     "Node1":"Test",
     "Node12":"Test",
     "Node2":"Reference",
     "Node3":"Reference",
     "Node8":"Test",
     "Node9":"Test",
     "PIG":"Reference",
     "RAT":"Reference",
     "RHMONKEY":"Test"
    }
  },
 "timers":{
   "General descriptive model fitting":{
     "order":2,
     "timer":159
    },
   "Overall":{
     "order":0,
     "timer":428
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":13
    },
   "RELAX alternative model fitting":{
     "order":3,
     "timer":61
    },
   "RELAX null model fitting":{
     "order":4,
     "timer":53
    },
   "RELAX partitioned descriptive":{
     "order":5,
     "timer":141
    }
  }
}