annotate test-data/relax-out1.json @ 5:bece0bad8e89 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e31ca8967662206fc17d608efea398502569437a"

{
 "analysis":{
   "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n                                                Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems",
   "version":"2.1",
   "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",
   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
   "contact":"[e-mail]",
   "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"
  },
 "input":{
   "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa",
   "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":-3531.964032193222,
     "estimated parameters":24,
     "AIC-c":7112.142925621896,
     "Equilibrium frequencies":[
      [0.3563279857397504],
      [0.1837789661319073],
      [0.2402852049910873],
      [0.2196078431372549]
      ],
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.264131123736109,
       "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388,
       "Substitution rate from nucleotide C to nucleotide T":1.017887589835735,
       "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065
      },
     "display order":0
    },
   "MG94xREV with separate rates for branch sets":{
     "Log Likelihood":-3460.931903299487,
     "estimated parameters":32,
     "AIC-c":6987.013507197776,
     "Equilibrium frequencies":[
      [0.04785168648208005],
      [0.03911346079312019],
      [0.04842054060317301],
      [0.04069665666515385],
      [0.01817010744778396],
      [0.01485205303123071],
      [0.01838611113045968],
      [0.01545321970309948],
      [0.0190138898893362],
      [0.01554175184587827],
      [0.01923992433904378],
      [0.01617083546230154],
      [0.02796925133965702],
      [0.02286176927319543],
      [0.02830174586718859],
      [0.02378714529482007],
      [0.01687870337957799],
      [0.01379647304851128],
      [0.01707935503225849],
      [0.01435491300079667],
      [0.006409133648843443],
      [0.005238757839512795],
      [0.006485324528555602],
      [0.005450807083377185],
      [0.006706760641638982],
      [0.005482034985409045],
      [0.006786489669196017],
      [0.005703931360295163],
      [0.009865581170012171],
      [0.008064021368173151],
      [0.009982861811889655],
      [0.008390428826966174],
      [0.03287895020631181],
      [0.02687490503171972],
      [0.033269810543681],
      [0.0279627207822247],
      [0.01248470225271473],
      [0.01020486315060615],
      [0.01263311863778268],
      [0.01061792547971484],
      [0.01306446616325414],
      [0.01067875601941112],
      [0.01321977470017749],
      [0.01111100011404158],
      [0.01921770557551369],
      [0.01570834862514353],
      [0.01944616295744266],
      [0.01634417558076203],
      [0.01975257768318274],
      [0.02055210293142003],
      [0.009176034326710849],
      [0.007500393094996483],
      [0.00928511773266342],
      [0.007803986567571961],
      [0.00784869593340758],
      [0.009716299514778986],
      [0.008166387662818644],
      [0.01412467213650941],
      [0.01154535713247913],
      [0.01429258425298098],
      [0.01201267864744234]
      ],
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *Reference*":[
        [1.617765969026557, 1]
        ],
       "non-synonymous/synonymous rate ratio for *Test*":[
        [0.7687683974183303, 1]
        ]
      },
     "display order":1
    },
   "General descriptive":{
     "Log Likelihood":-3420.975369746331,
     "estimated parameters":51,
     "AIC-c":6946.868231241836,
     "Rate Distributions":{
       "Shared":{
         "0":{
           "omega":1e-08,
           "proportion":0.2345034364701236
          },
         "1":{
           "omega":1e-08,
           "proportion":0.3180344596999608
          },
         "2":{
           "omega":6.64943557055033,
           "proportion":0.4474621038299156
          }
        }
      },
     "display order":4
    },
   "RELAX alternative":{
     "Log Likelihood":-3429.125323833579,
     "estimated parameters":36,
     "AIC-c":6931.704002822642,
     "Rate Distributions":{
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.1993913071931658
          },
         "1":{
           "omega":0,
           "proportion":0.3360341729181165
          },
         "2":{
           "omega":2.153056268947235,
           "proportion":0.4645745198887177
          }
        },
       "Reference":{
         "0":{
           "omega":0,
           "proportion":0.1993913071931658
          },
         "1":{
           "omega":0,
           "proportion":0.3360341729181165
          },
         "2":{
           "omega":6.166712663934246,
           "proportion":0.4645745198887177
          }
        }
      },
     "display order":2
    },
   "RELAX null":{
     "Log Likelihood":-3437.187429488768,
     "estimated parameters":35,
     "AIC-c":6945.748904779063,
     "Rate Distributions":{
       "Test":{
         "0":{
           "omega":0.1177689533662908,
           "proportion":0.4926494715348529
          },
         "1":{
           "omega":0.3195682613972807,
           "proportion":0.1517366025099117
          },
         "2":{
           "omega":3.893733071412322,
           "proportion":0.3556139259552353
          }
        },
       "Reference":{
         "0":{
           "omega":0.1177689533662908,
           "proportion":0.4926494715348529
          },
         "1":{
           "omega":0.3195682613972807,
           "proportion":0.1517366025099117
          },
         "2":{
           "omega":3.893733071412322,
           "proportion":0.3556139259552353
          }
        }
      },
     "display order":3
    },
   "RELAX partitioned descriptive":{
     "Log Likelihood":-3427.515821600644,
     "estimated parameters":40,
     "AIC-c":6936.824972889643,
     "Rate Distributions":{
       "Test":{
         "0":{
           "omega":0.2264899618249929,
           "proportion":0.1370778077745601
          },
         "1":{
           "omega":0.2328054750512875,
           "proportion":0.6322930022247097
          },
         "2":{
           "omega":4.13407071706127,
           "proportion":0.2306291900007301
          }
        },
       "Reference":{
         "0":{
           "omega":0,
           "proportion":0.09054841512283768
          },
         "1":{
           "omega":0,
           "proportion":0.4231976237742962
          },
         "2":{
           "omega":5.975493863572218,
           "proportion":0.4862539611028661
          }
        }
      },
     "display order":5
    }
  },
 "timers":{
   "Overall":{
     "timer":562,
     "order":0
    },
   "Preliminary model fitting":{
     "timer":33,
     "order":1
    },
   "General descriptive model fitting":{
     "timer":256,
     "order":2
    },
   "RELAX alternative model fitting":{
     "timer":78,
     "order":3
    },
   "RELAX null model fitting":{
     "timer":98,
     "order":4
    },
   "RELAX partitioned descriptive":{
     "timer":95,
     "order":5
    }
  },
 "test results":{
   "LRT":16.12421131037809,
   "p-value":5.932080525117289e-05,
   "relaxation or intensification parameter":0.4215604262166031
  },
 "tested":{
   "0":{
     "Pig":"Test",
     "Cow":"Reference",
     "Node3":"Test",
     "Horse":"Reference",
     "Cat":"Reference",
     "Node2":"Test",
     "RhMonkey":"Test",
     "Baboon":"Test",
     "Node9":"Test",
     "Human":"Test",
     "Chimp":"Test",
     "Node12":"Test",
     "Node8":"Test",
     "Node1":"Test",
     "Rat":"Test",
     "Mouse":"Test"
    }
  },
 "data partitions":{
   "0":{
     "name":"relax.filter.default",
     "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]
      ]
    }
  },
 "branch attributes":{
   "0":{
     "Human":{
       "original name":"Human",
       "Nucleotide GTR":0,
       "MG94xREV with separate rates for branch sets":0,
       "General descriptive":0,
       "k (general descriptive)":0.7168352052656061,
       "RELAX alternative":0,
       "RELAX null":0,
       "RELAX partitioned descriptive":0
      },
     "Chimp":{
       "original name":"Chimp",
       "Nucleotide GTR":0.001818722292071369,
       "MG94xREV with separate rates for branch sets":0.001828056639868651,
       "General descriptive":0.001850581335499795,
       "k (general descriptive)":2.329184252362038,
       "RELAX alternative":0.001831548027528597,
       "RELAX null":0.001835680183060623,
       "RELAX partitioned descriptive":0.00183255534978807
      },
     "Baboon":{
       "original name":"Baboon",
       "Nucleotide GTR":0.001682319705247233,
       "MG94xREV with separate rates for branch sets":0.001770013551346919,
       "General descriptive":0.001869883333754939,
       "k (general descriptive)":0.1228116964827354,
       "RELAX alternative":0.001867314836287998,
       "RELAX null":0.001853697678697539,
       "RELAX partitioned descriptive":0.00189422569191071
      },
     "RhMonkey":{
       "original name":"RhMonkey",
       "Nucleotide GTR":0.003776495523121213,
       "MG94xREV with separate rates for branch sets":0.003720554271464007,
       "General descriptive":0.003663070393385353,
       "k (general descriptive)":2.272939790126477,
       "RELAX alternative":0.003641537789305734,
       "RELAX null":0.003670955010908306,
       "RELAX partitioned descriptive":0.003632158699516803
      },
     "Cow":{
       "original name":"Cow",
       "Nucleotide GTR":0.2483201583381086,
       "MG94xREV with separate rates for branch sets":0.2522875145085426,
       "General descriptive":0.3735091756053704,
       "k (general descriptive)":1.19957642031092,
       "RELAX alternative":0.3407703477665083,
       "RELAX null":0.2958310860090909,
       "RELAX partitioned descriptive":0.3460604457589064
      },
     "Pig":{
       "original name":"Pig",
       "Nucleotide GTR":0.1871417867164377,
       "MG94xREV with separate rates for branch sets":0.1903173961963296,
       "General descriptive":0.2109384940367451,
       "k (general descriptive)":0.6656155688777629,
       "RELAX alternative":0.197167672065417,
       "RELAX null":0.2182629931612711,
       "RELAX partitioned descriptive":0.2076369268997903
      },
     "Horse":{
       "original name":"Horse",
       "Nucleotide GTR":0.2091567334932583,
       "MG94xREV with separate rates for branch sets":0.2159358728261337,
       "General descriptive":0.2810540078141565,
       "k (general descriptive)":0.8115699858212525,
       "RELAX alternative":0.3032889682089364,
       "RELAX null":0.2571098559672552,
       "RELAX partitioned descriptive":0.3026705354406338
      },
     "Cat":{
       "original name":"Cat",
       "Nucleotide GTR":0.2660040109418023,
       "MG94xREV with separate rates for branch sets":0.2795692100037539,
       "General descriptive":0.3635335087937213,
       "k (general descriptive)":0.9728289997736356,
       "RELAX alternative":0.3660889485578829,
       "RELAX null":0.3281803512051322,
       "RELAX partitioned descriptive":0.370631318143086
      },
     "Mouse":{
       "original name":"Mouse",
       "Nucleotide GTR":0.1182531454610134,
       "MG94xREV with separate rates for branch sets":0.1199409901922202,
       "General descriptive":0.1313354563273305,
       "k (general descriptive)":0.2294495132372282,
       "RELAX alternative":0.1341640738853253,
       "RELAX null":0.1483938193994467,
       "RELAX partitioned descriptive":0.1476318125310598
      },
     "Rat":{
       "original name":"Rat",
       "Nucleotide GTR":0.06669544716210057,
       "MG94xREV with separate rates for branch sets":0.06725647453745125,
       "General descriptive":0.07175915155128718,
       "k (general descriptive)":0.5208088414555363,
       "RELAX alternative":0.0724007498013708,
       "RELAX null":0.07365614414375878,
       "RELAX partitioned descriptive":0.07568744563050285
      },
     "Node1":{
       "Nucleotide GTR":0.2771601504028877,
       "MG94xREV with separate rates for branch sets":0.286127507474972,
       "General descriptive":0.3532216661512288,
       "k (general descriptive)":0.2199586786715634,
       "RELAX alternative":0.3833004811985787,
       "RELAX null":0.4576044234710181,
       "RELAX partitioned descriptive":0.4360897576025625
      },
     "Node12":{
       "Nucleotide GTR":0.01783222754921504,
       "MG94xREV with separate rates for branch sets":0.01799298835381691,
       "General descriptive":0.01771170858901891,
       "k (general descriptive)":0.1560499010177516,
       "RELAX alternative":0.01833338832069913,
       "RELAX null":0.01828012634520382,
       "RELAX partitioned descriptive":0.01877701767421286
      },
     "Node2":{
       "Nucleotide GTR":0.06619118337434968,
       "MG94xREV with separate rates for branch sets":0.06192085035608558,
       "General descriptive":0.05843310574046084,
       "k (general descriptive)":0.2816499194095207,
       "RELAX alternative":0.05469841675490748,
       "RELAX null":0.06219694236954142,
       "RELAX partitioned descriptive":0.06011281230238084
      },
     "Node3":{
       "Nucleotide GTR":0.09883746945145887,
       "MG94xREV with separate rates for branch sets":0.09744342239018626,
       "General descriptive":0.1340338084149808,
       "k (general descriptive)":0.8358980179450297,
       "RELAX alternative":0.1164056814082033,
       "RELAX null":0.1282588343299434,
       "RELAX partitioned descriptive":0.1194563668460339
      },
     "Node8":{
       "Nucleotide GTR":0.106110061225871,
       "MG94xREV with separate rates for branch sets":0.1090208137603471,
       "General descriptive":0.1401594332730181,
       "k (general descriptive)":0.9135621448569878,
       "RELAX alternative":0.1275155316795084,
       "RELAX null":0.1346842719904758,
       "RELAX partitioned descriptive":0.1358683972849559
      },
     "Node9":{
       "Nucleotide GTR":0.02567391471029082,
       "MG94xREV with separate rates for branch sets":0.02582385148170195,
       "General descriptive":0.02665352479510937,
       "k (general descriptive)":0.1089752436854629,
       "RELAX alternative":0.02681134359856903,
       "RELAX null":0.02759760291393045,
       "RELAX partitioned descriptive":0.02746061131173372
      }
    },
   "attributes":{
     "original name":{
       "attribute type":"node label",
       "display order":-1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "General descriptive":{
       "attribute type":"branch length",
       "display order":4
      },
     "k (general descriptive)":{
       "attribute type":"branch label",
       "display order":4
      },
     "RELAX alternative":{
       "attribute type":"branch length",
       "display order":2
      },
     "RELAX null":{
       "attribute type":"branch length",
       "display order":3
      },
     "RELAX partitioned descriptive":{
       "attribute type":"branch length",
       "display order":5
      }
    }
  }
}