annotate test-data/relax-out2-1.json @ 35:35723f87964d draft default tip

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

{
 "analysis":0,
 "branch attributes":{
   "0":{
     "BABOON":{
       "General descriptive":0.001858528201768933,
       "MG94xREV with separate rates for branch sets":0.001729040005725717,
       "Nucleotide GTR":0.001685167654714891,
       "RELAX alternative":0.001823573976182991,
       "RELAX null":0.001855504238020734,
       "RELAX partitioned descriptive":0.001856473113608415,
       "k (general descriptive)":0.09974837182960776,
       "original name":"BABOON"
      },
     "CAT":{
       "General descriptive":0.3649687317465272,
       "MG94xREV with separate rates for branch sets":0.2761191158060541,
       "Nucleotide GTR":0.2660536011315811,
       "RELAX alternative":0.3317928646169214,
       "RELAX null":0.3252639231399129,
       "RELAX partitioned descriptive":0.3330192884009499,
       "k (general descriptive)":2.321295373553348,
       "original name":"CAT"
      },
     "CHIMP":{
       "General descriptive":0.00184909269599246,
       "MG94xREV with separate rates for branch sets":0.001822551054713939,
       "Nucleotide GTR":0.001820258053351119,
       "RELAX alternative":0.00182628703877269,
       "RELAX null":0.001834608540291232,
       "RELAX partitioned descriptive":0.001827445389436029,
       "k (general descriptive)":5.301733626197528,
       "original name":"CHIMP"
      },
     "COW":{
       "General descriptive":0.3735020294731436,
       "MG94xREV with separate rates for branch sets":0.248802707042435,
       "Nucleotide GTR":0.2480198736772598,
       "RELAX alternative":0.3080684096213485,
       "RELAX null":0.2951198100127046,
       "RELAX partitioned descriptive":0.3113651933641743,
       "k (general descriptive)":2.848124116654745,
       "original name":"COW"
      },
     "HORSE":{
       "General descriptive":0.2803565521817367,
       "MG94xREV with separate rates for branch sets":0.2114983058912022,
       "Nucleotide GTR":0.2090998951755368,
       "RELAX alternative":0.2669775401023034,
       "RELAX null":0.2560153217844985,
       "RELAX partitioned descriptive":0.2711533659241344,
       "k (general descriptive)":1.929084551844662,
       "original name":"HORSE"
      },
     "HUMAN":{
       "General descriptive":0,
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":0,
       "RELAX alternative":0,
       "RELAX null":0,
       "RELAX partitioned descriptive":0,
       "k (general descriptive)":1.417418953564817,
       "original name":"HUMAN"
      },
     "MOUSE":{
       "General descriptive":0.1308909653091745,
       "MG94xREV with separate rates for branch sets":0.1192893635530923,
       "Nucleotide GTR":0.1181058300538561,
       "RELAX alternative":0.15085996133762,
       "RELAX null":0.1469017908982058,
       "RELAX partitioned descriptive":0.1491287772297175,
       "k (general descriptive)":0.4628338932722805,
       "original name":"MOUSE"
      },
     "Node1":{
       "General descriptive":0.3501950875747647,
       "MG94xREV with separate rates for branch sets":0.2891531817656844,
       "Nucleotide GTR":0.2767105173979571,
       "RELAX alternative":0.3644026907015058,
       "RELAX null":0.4527247199492397,
       "RELAX partitioned descriptive":0.4226204412177209,
       "k (general descriptive)":0.4559088158670693
      },
     "Node12":{
       "General descriptive":0.01767952779767795,
       "MG94xREV with separate rates for branch sets":0.0175770110347634,
       "Nucleotide GTR":0.01784222107494562,
       "RELAX alternative":0.0176558660351027,
       "RELAX null":0.01825591179366154,
       "RELAX partitioned descriptive":0.01814639835827904,
       "k (general descriptive)":0.1240838029653794
      },
     "Node2":{
       "General descriptive":0.05770620828101171,
       "MG94xREV with separate rates for branch sets":0.06229443926236622,
       "Nucleotide GTR":0.06614755778044307,
       "RELAX alternative":0.05866256113025137,
       "RELAX null":0.06147496751530821,
       "RELAX partitioned descriptive":0.05724188758009503,
       "k (general descriptive)":0.5371848217199983
      },
     "Node3":{
       "General descriptive":0.1330354609631224,
       "MG94xREV with separate rates for branch sets":0.1003154990002797,
       "Nucleotide GTR":0.09883748387954429,
       "RELAX alternative":0.1265135269643693,
       "RELAX null":0.1276253046950155,
       "RELAX partitioned descriptive":0.1271876163104063,
       "k (general descriptive)":1.981364628056296
      },
     "Node8":{
       "General descriptive":0.140369727816558,
       "MG94xREV with separate rates for branch sets":0.1127066220459272,
       "Nucleotide GTR":0.1062201244057951,
       "RELAX alternative":0.1280322211601967,
       "RELAX null":0.1343412714385626,
       "RELAX partitioned descriptive":0.1406663540457613,
       "k (general descriptive)":2.211767324109487
      },
     "Node9":{
       "General descriptive":0.02663291940160552,
       "MG94xREV with separate rates for branch sets":0.02627402966233569,
       "Nucleotide GTR":0.02567813733543303,
       "RELAX alternative":0.02720907734174326,
       "RELAX null":0.02752483699250281,
       "RELAX partitioned descriptive":0.02810928828288993,
       "k (general descriptive)":0.07329530197274074
      },
     "PIG":{
       "General descriptive":0.2104965149960229,
       "MG94xREV with separate rates for branch sets":0.1921302603267553,
       "Nucleotide GTR":0.1871390433004313,
       "RELAX alternative":0.2174541263946326,
       "RELAX null":0.2166570805170097,
       "RELAX partitioned descriptive":0.2198382730708073,
       "k (general descriptive)":1.581624239713873,
       "original name":"PIG"
      },
     "RAT":{
       "General descriptive":0.07156643194841542,
       "MG94xREV with separate rates for branch sets":0.06831927364558048,
       "Nucleotide GTR":0.06661490534189227,
       "RELAX alternative":0.07273892007491474,
       "RELAX null":0.07342001791171293,
       "RELAX partitioned descriptive":0.07588524426470618,
       "k (general descriptive)":1.318666444029934,
       "original name":"RAT"
      },
     "RHMONKEY":{
       "General descriptive":0.003670942377703963,
       "MG94xREV with separate rates for branch sets":0.003755247927570558,
       "Nucleotide GTR":0.003778804730491441,
       "RELAX alternative":0.003673289414323487,
       "RELAX null":0.003666197747079884,
       "RELAX partitioned descriptive":0.003661285250492945,
       "k (general descriptive)":5.244027200799457,
       "original name":"RHMONKEY"
      }
    },
   "attributes":{
     "General descriptive":{
       "attribute type":"branch length",
       "display order":4
      },
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "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
      },
     "k (general descriptive)":{
       "attribute type":"branch label",
       "display order":4
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
  },
 "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":"relax.filter.default"
    }
  },
 "fits":{
   "General descriptive":{
     "AIC-c":6945.887251511141,
     "Log Likelihood":-3420.484879880983,
     "Rate Distributions":{
       "Shared":{
         "0":{
           "omega":2.201644423775106e-18,
           "proportion":0.1667516969215508
          },
         "1":{
           "omega":2.201644423775106e-18,
           "proportion":0.3790423141178453
          },
         "2":{
           "omega":2.201644241390081,
           "proportion":0.4542059889606039
          }
        }
      },
     "display order":4,
     "estimated parameters":51
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6987.278076404838,
     "Equilibrium frequencies":      [
[0.04876086397632926],
      [0.03982224127745371],
      [0.0494959405650269],
      [0.04152830682371345],
      [0.01810345074594235],
      [0.01478480742075003],
      [0.01837636270304883],
      [0.01541821854326533],
      [0.01892910005547028],
      [0.01545910240515689],
      [0.01921445878706794],
      [0.01612140169177368],
      [0.02829747763884322],
      [0.02311011106415996],
      [0.02872406592369408],
      [0.02410019507229243],
      [0.01663805943190806],
      [0.01358804506433061],
      [0.01688888041768248],
      [0.01417018446135155],
      [0.006177213955434187],
      [0.005044834822351987],
      [0.006270336287397383],
      [0.00526096577332031],
      [0.006458939937330408],
      [0.005274916061901906],
      [0.006556309326397028],
      [0.005500904159606446],
      [0.009655594186286731],
      [0.007885574003572761],
      [0.009801153568494354],
      [0.008223407979974132],
      [0.03327785448210915],
      [0.02717750758119989],
      [0.03377952261833742],
      [0.02834184710178207],
      [0.01235507229404208],
      [0.01009019590244688],
      [0.01254132667213156],
      [0.01052248035033209],
      [0.01291855364640413],
      [0.01055038238273567],
      [0.01311330258173711],
      [0.01100238215235291],
      [0.01931219560697892],
      [0.0157719705998612],
      [0.01960332955558842],
      [0.01644767379420349],
      [0.01965132601881859],
      [0.02049322866376102],
      [0.008933621043463411],
      [0.007295949736387736],
      [0.009068296583349953],
      [0.007608523013862737],
      [0.007628698224327205],
      [0.009481877006094248],
      [0.00795552712159237],
      [0.01396413011303752],
      [0.01140428846505027],
      [0.01417464125436193],
      [0.01189287130232129] 
      ],
     "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] 
        ]
      },
     "display order":1,
     "estimated parameters":32
    },
   "Nucleotide GTR":{
     "AIC-c":7112.857288723968,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "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":{
     "AIC-c":6938.419285358699,
     "Log Likelihood":-3432.482965101608,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0,
           "proportion":0.2968543549269862
          },
         "1":{
           "omega":0,
           "proportion":0.2447083724876047
          },
         "2":{
           "omega":3.910413867333085,
           "proportion":0.4584372725854091
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.2968543549269862
          },
         "1":{
           "omega":0,
           "proportion":0.2447083724876047
          },
         "2":{
           "omega":1.655264242043239,
           "proportion":0.4584372725854091
          }
        }
      },
     "display order":2,
     "estimated parameters":36
    },
   "RELAX null":{
     "AIC-c":6946.046147526199,
     "Log Likelihood":-3437.336050862336,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0.07516343499603452,
           "proportion":0.2524283429126023
          },
         "1":{
           "omega":0.1730729265669467,
           "proportion":0.3734402861071174
          },
         "2":{
           "omega":3.70326279512502,
           "proportion":0.3741313709802804
          }
        },
       "Test":{
         "0":{
           "omega":0.07516343499603452,
           "proportion":0.2524283429126023
          },
         "1":{
           "omega":0.1730729265669467,
           "proportion":0.3734402861071174
          },
         "2":{
           "omega":3.70326279512502,
           "proportion":0.3741313709802804
          }
        }
      },
     "display order":3,
     "estimated parameters":35
    },
   "RELAX partitioned descriptive":{
     "AIC-c":6944.507313452719,
     "Log Likelihood":-3431.356991882183,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0,
           "proportion":0.3694476627871225
          },
         "1":{
           "omega":0.03660893085044142,
           "proportion":0.1726741298596992
          },
         "2":{
           "omega":3.988980749944551,
           "proportion":0.4578782073531784
          }
        },
       "Test":{
         "0":{
           "omega":0.224878249826745,
           "proportion":0.2953732524277409
          },
         "1":{
           "omega":0.231175241198686,
           "proportion":0.5325206774143161
          },
         "2":{
           "omega":4.178788461910403,
           "proportion":0.172106070157943
          }
        }
      },
     "display order":5,
     "estimated parameters":40
    }
  },
 "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)"
    }
  },
 "runtime":"2.5.36",
 "test results":{
   "LRT":9.706171521456781,
   "p-value":0.001836502097725456,
   "relaxation or intensification parameter":0.3695692925647034
  },
 "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
    }
  }
}