annotate test-data/busted-out1.json @ 9:0669558ebc6b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"

{
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  ],
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
   "contact":"[e-mail]",
   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "version":"3.0"
  },
 "background":0,
 "branch attributes":{
   "0":{
     "Baboon":{
       "MG94xREV with separate rates for branch sets":0.001771850913718116,
       "Nucleotide GTR":0.00167976779100812,
       "constrained":0.0005055252388761481,
       "original name":"Baboon",
       "unconstrained":0.0005398732671668005
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     "Cat":{
       "MG94xREV with separate rates for branch sets":0.2738959056554072,
       "Nucleotide GTR":0.266075486389923,
       "constrained":0.1152712488116292,
       "original name":"Cat",
       "unconstrained":0.120218071527276
      },
     "Chimp":{
       "MG94xREV with separate rates for branch sets":0.001827968855137289,
       "Nucleotide GTR":0.001817801565830578,
       "constrained":0.0006181497274348637,
       "original name":"Chimp",
       "unconstrained":0.0006183542388399873
      },
     "Cow":{
       "MG94xREV with separate rates for branch sets":0.2477119781238836,
       "Nucleotide GTR":0.2480176045457076,
       "constrained":0.1036665344622347,
       "original name":"Cow",
       "unconstrained":0.1088268022245659
      },
     "Horse":{
       "MG94xREV with separate rates for branch sets":0.211203801568566,
       "Nucleotide GTR":0.2090856782081004,
       "constrained":0.08236651201101133,
       "original name":"Horse",
       "unconstrained":0.08564084427400141
      },
     "Human":{
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":0,
       "constrained":0,
       "original name":"Human",
       "unconstrained":0
      },
     "Mouse":{
       "MG94xREV with separate rates for branch sets":0.1200702443392807,
       "Nucleotide GTR":0.1181301915748399,
       "constrained":0.04601717170435755,
       "original name":"Mouse",
       "unconstrained":0.04942545223877414
      },
     "Node1":{
       "MG94xREV with separate rates for branch sets":0.2837967450491412,
       "Nucleotide GTR":0.2767871391397028,
       "constrained":0.1295742765519239,
       "unconstrained":0.1515367890887531
      },
     "Node12":{
       "MG94xREV with separate rates for branch sets":0.01788296579298991,
       "Nucleotide GTR":0.01784443144961206,
       "constrained":0.005338125135456628,
       "unconstrained":0.00572208893382143
      },
     "Node2":{
       "MG94xREV with separate rates for branch sets":0.06423714540466627,
       "Nucleotide GTR":0.06616183769400197,
       "constrained":0.02253286838656328,
       "unconstrained":0.02248978054488407
      },
     "Node3":{
       "MG94xREV with separate rates for branch sets":0.1017201477652066,
       "Nucleotide GTR":0.09890202668045614,
       "constrained":0.04280347934583096,
       "unconstrained":0.04618990784049085
      },
     "Node8":{
       "MG94xREV with separate rates for branch sets":0.1096720572321177,
       "Nucleotide GTR":0.10624077635158,
       "constrained":0.04415239867414091,
       "unconstrained":0.04768889036449767
      },
     "Node9":{
       "MG94xREV with separate rates for branch sets":0.02591275475412757,
       "Nucleotide GTR":0.02566524291670843,
       "constrained":0.00997308939110993,
       "unconstrained":0.009841415288506062
      },
     "Pig":{
       "MG94xREV with separate rates for branch sets":0.1928073761020463,
       "Nucleotide GTR":0.1871746592118726,
       "constrained":0.07816490289585476,
       "original name":"Pig",
       "unconstrained":0.08275992348314189
      },
     "Rat":{
       "MG94xREV with separate rates for branch sets":0.06698958986289986,
       "Nucleotide GTR":0.06656862018951525,
       "constrained":0.02277034233250765,
       "original name":"Rat",
       "unconstrained":0.02372534359054489
      },
     "RhMonkey":{
       "MG94xREV with separate rates for branch sets":0.003717482368324115,
       "Nucleotide GTR":0.003775504255522691,
       "constrained":0.001359450941376631,
       "original name":"RhMonkey",
       "unconstrained":0.00132482447204072
      }
    },
   "attributes":{
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "constrained":{
       "attribute type":"branch length",
       "display order":1
      },
     "original name":{
       "attribute type":"node label",
       "display order":0
      },
     "unconstrained":{
       "attribute type":"branch length",
       "display order":0
      }
    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] 
      ],
     "name":"busted.filter.default"
    }
  },
 "fits":{
   "Constrained model":{
     "AIC-c":6918.851822592964,
     "Log Likelihood":-3419.573452280089,
     "Rate Distributions":{
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.3289898788632067,
           "rate":0.3124849036133048
          },
         "1":{
           "proportion":0.5748197734913485,
           "rate":1.039520868895482
          },
         "2":{
           "proportion":0.09619034764544485,
           "rate":3.115265578623139
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.02093092071081848
          },
         "1":{
           "omega":0,
           "proportion":0.1387433808480476
          },
         "2":{
           "omega":1,
           "proportion":0.8403256984411339
          }
        }
      },
     "display order":3,
     "estimated parameters":39
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6997.089050462658,
     "Equilibrium frequencies":      [
[0.04875339327772683],
      [0.03982858547830345],
      [0.04946803524790992],
      [0.04152216138298744],
      [0.01811683453600613],
      [0.01480036248560469],
      [0.0183823965708893],
      [0.01542969784826435],
      [0.01894694796506697],
      [0.01547851515238824],
      [0.01922467805342367],
      [0.01613668666381816],
      [0.02832099415740372],
      [0.02313654621336914],
      [0.02873613184734657],
      [0.02412034959764736],
      [0.01662182431200483],
      [0.01357902918971745],
      [0.01686547203528639],
      [0.01415643148428886],
      [0.006176695005242439],
      [0.005045987744654046],
      [0.006267234867003878],
      [0.005260551308914496],
      [0.006459711194459957],
      [0.005277194922783805],
      [0.006554399593040238],
      [0.005501589790395056],
      [0.009655668202293983],
      [0.007888099278638223],
      [0.009797203904398108],
      [0.008223514024394991],
      [0.03326722643528176],
      [0.02717732003095303],
      [0.03375486749252685],
      [0.02833294365668738],
      [0.01236215156074466],
      [0.01009913314808799],
      [0.01254335971371867],
      [0.01052856463184265],
      [0.01292858539344675],
      [0.0105618754683007],
      [0.0131180965046964],
      [0.01101098350431497],
      [0.0193250328267319],
      [0.01578738770911659],
      [0.0196083049972345],
      [0.01645869298147252],
      [0.01962343746171723],
      [0.02045785777700414],
      [0.008926115885166477],
      [0.007292098982657142],
      [0.009056957588961733],
      [0.007602170831388156],
      [0.007626222986467745],
      [0.009471947420992787],
      [0.007950502328516303],
      [0.01395367801862353],
      [0.01139931439306339],
      [0.01415821524731906],
      [0.01188403168729233] 
      ],
     "Log Likelihood":-3467.004808147542,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.9950576192409499, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":31
    },
   "Nucleotide GTR":{
     "AIC-c":7112.85745601076,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "Log Likelihood":-3532.321297387654,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,
       "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,
       "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,
       "Substitution rate from nucleotide G to nucleotide T":0.304615404570875
      },
     "display order":0,
     "estimated parameters":24
    },
   "Unconstrained model":{
     "AIC-c":6910.766610587704,
     "Log Likelihood":-3414.486640449675,
     "Rate Distributions":{
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.2645541257391169,
           "rate":0.2747941124675511
          },
         "1":{
           "proportion":0.6325830460054784,
           "rate":0.9734675888351726
          },
         "2":{
           "proportion":0.1028628282554047,
           "rate":3.028333913894314
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.04809457608200497
          },
         "1":{
           "omega":0,
           "proportion":0.3410012743721951
          },
         "2":{
           "omega":1.89363684081788,
           "proportion":0.6109041495458
          }
        }
      },
     "display order":2,
     "estimated parameters":40
    }
  },
 "input":{
   "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",
   "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)"
    }
  },
 "test results":{
   "LRT":10.17362366082671,
   "p-value":0.003088842014430382
  },
 "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"
    }
  },
 "timers":{
   "Constrained BUSTED model fitting":{
     "order":3,
     "timer":62
    },
   "Overall":{
     "order":0,
     "timer":228
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":3
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":161
    }
  }
}