annotate test-data/relax-out1.json @ 34:6e72195b364a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d

{
 "analysis":0,
 "branch attributes":{
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       "MG94xREV with separate rates for branch sets":0.001769294089885709,
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     "Chimp":{
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       "MG94xREV with separate rates for branch sets":0.001826027667597702,
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     "Cow":{
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       "MG94xREV with separate rates for branch sets":0.2521304147607955,
       "Nucleotide GTR":0.2480198736772598,
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       "RELAX partitioned descriptive":0.3469082289876269,
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     "Horse":{
       "General descriptive":0.2804279827409984,
       "MG94xREV with separate rates for branch sets":0.2158535884657318,
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       "RELAX alternative":0.3058441352816696,
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     "Human":{
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       "MG94xREV with separate rates for branch sets":0,
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     "Mouse":{
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       "Nucleotide GTR":0.1181058300538561,
       "RELAX alternative":0.1346294129227689,
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       "original name":"Mouse"
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       "General descriptive":0.3500691487967139,
       "MG94xREV with separate rates for branch sets":0.2856782993656827,
       "Nucleotide GTR":0.2767105173979571,
       "RELAX alternative":0.385503346940632,
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       "General descriptive":0.01767932040676307,
       "MG94xREV with separate rates for branch sets":0.01800350744117403,
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       "General descriptive":0.1330088052861041,
       "MG94xREV with separate rates for branch sets":0.09733132151710643,
       "Nucleotide GTR":0.09883748387954429,
       "RELAX alternative":0.1169235247351394,
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     "Node8":{
       "General descriptive":0.140412283431793,
       "MG94xREV with separate rates for branch sets":0.1091939823455765,
       "Nucleotide GTR":0.1062201244057951,
       "RELAX alternative":0.1284192265733904,
       "RELAX null":0.1334227466998376,
       "RELAX partitioned descriptive":0.1367904558404228,
       "k (general descriptive)":2.206967022203622
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     "Node9":{
       "General descriptive":0.02664133794298214,
       "MG94xREV with separate rates for branch sets":0.02578742148415842,
       "Nucleotide GTR":0.02567813733543303,
       "RELAX alternative":0.02680940150436639,
       "RELAX null":0.0273694783141817,
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     "Pig":{
       "General descriptive":0.210591346560755,
       "MG94xREV with separate rates for branch sets":0.1903463787974325,
       "Nucleotide GTR":0.1871390433004313,
       "RELAX alternative":0.1974790507889271,
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       "RELAX partitioned descriptive":0.2084407457285946,
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       "General descriptive":0.07157977734335202,
       "MG94xREV with separate rates for branch sets":0.06709765698107663,
       "Nucleotide GTR":0.06661490534189227,
       "RELAX alternative":0.07252374836036582,
       "RELAX null":0.0734705682786943,
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     "RhMonkey":{
       "General descriptive":0.003672848089716511,
       "MG94xREV with separate rates for branch sets":0.003717350789869306,
       "Nucleotide GTR":0.003778804730491441,
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       "RELAX null":0.003661271320845124,
       "RELAX partitioned descriptive":0.003625957794514879,
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       "original name":"RhMonkey"
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   "attributes":{
     "General descriptive":{
       "attribute type":"branch length",
       "display order":4
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     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
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     "Nucleotide GTR":{
       "attribute type":"branch length",
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     "RELAX alternative":{
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     "RELAX null":{
       "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",
       "display order":-1
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 "data partitions":{
   "0":{
     "coverage":      [
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      ],
     "name":"relax.filter.default"
    }
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 "fits":{
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     "Log Likelihood":-3420.487593043145,
     "Rate Distributions":{
       "Shared":{
         "0":{
           "omega":2.201451464048879e-18,
           "proportion":0.3073650505039141
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         "1":{
           "omega":2.201451464048879e-18,
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           "proportion":0.4542458006324541
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     "estimated parameters":51
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   "MG94xREV with separate rates for branch sets":{
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     "Equilibrium frequencies":      [
[0.04876086397632926],
      [0.03982224127745371],
      [0.0494959405650269],
      [0.04152830682371345],
      [0.01810345074594235],
      [0.01478480742075003],
      [0.01837636270304883],
      [0.01541821854326533],
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      [0.005274916061901906],
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      [0.005500904159606446],
      [0.009655594186286731],
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      [0.01009019590244688],
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      [0.01931219560697892],
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      [0.01396413011303752],
      [0.01140428846505027],
      [0.01417464125436193],
      [0.01189287130232129] 
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     "Log Likelihood":-3461.208406480981,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *Reference*":        [
[0.7685912547191639, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *Test*":        [
[1.603198088111489, 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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      [0.2187728937728937] 
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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
      },
     "display order":0,
     "estimated parameters":24
    },
   "RELAX alternative":{
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     "Log Likelihood":-3429.236709163995,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":1.761161171239182e-19,
           "proportion":0.2691773911207853
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         "1":{
           "omega":1.762922332410267e-19,
           "proportion":0.2692122656891806
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         "2":{
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           "proportion":0.4616103431900341
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       "Test":{
         "0":{
           "omega":1.673670300056362e-44,
           "proportion":0.2691773911207853
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         "1":{
           "omega":1.677579612236672e-44,
           "proportion":0.2692122656891806
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         "2":{
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           "proportion":0.4616103431900341
          }
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     "display order":2,
     "estimated parameters":36
    },
   "RELAX null":{
     "AIC-c":6946.648596594286,
     "Log Likelihood":-3437.63727539638,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":1.408928936991542e-20,
           "proportion":0.265244047162938
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         "1":{
           "omega":1.410337865928411e-20,
           "proportion":0.28512630848952
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         "2":{
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           "proportion":0.4496296443475419
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       "Test":{
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         "1":{
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           "proportion":0.28512630848952
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           "proportion":0.4496296443475419
          }
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     "display order":3,
     "estimated parameters":35
    },
   "RELAX partitioned descriptive":{
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     "Log Likelihood":-3427.627954124649,
     "Rate Distributions":{
       "Reference":{
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           "proportion":0.4766160247339328
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         "1":{
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           "proportion":0.3005513276312735
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         "2":{
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           "proportion":0.2228326476347937
          }
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       "Test":{
         "0":{
           "omega":1.127143149593234e-21,
           "proportion":0.2367540589657237
          },
         "1":{
           "omega":1.128270292740756e-21,
           "proportion":0.2771164325302933
          },
         "2":{
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           "proportion":0.4861295085039831
          }
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     "display order":5,
     "estimated parameters":40
    }
  },
 "input":{
   "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/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)"
    }
  },
 "runtime":"2.5.32",
 "test results":{
   "LRT":16.80113246476958,
   "p-value":4.150852429507523e-05,
   "relaxation or intensification parameter":2.334214628944839
  },
 "tested":{
   "0":{
     "Baboon":"Reference",
     "Cat":"Test",
     "Chimp":"Reference",
     "Cow":"Test",
     "Horse":"Test",
     "Human":"Reference",
     "Mouse":"Reference",
     "Node1":"Reference",
     "Node12":"Reference",
     "Node2":"Reference",
     "Node3":"Reference",
     "Node8":"Reference",
     "Node9":"Reference",
     "Pig":"Reference",
     "Rat":"Reference",
     "RhMonkey":"Reference"
    }
  },
 "timers":{
   "General descriptive model fitting":{
     "order":2,
     "timer":127
    },
   "Overall":{
     "order":0,
     "timer":396
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":8
    },
   "RELAX alternative model fitting":{
     "order":3,
     "timer":103
    },
   "RELAX null model fitting":{
     "order":4,
     "timer":41
    },
   "RELAX partitioned descriptive":{
     "order":5,
     "timer":116
    }
  }
}