annotate test-data/relax-out2-1.json @ 33:365e33adf3a4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"

{
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       "MG94xREV with separate rates for branch sets":0.003755247927570558,
       "Nucleotide GTR":0.003778804730491441,
       "RELAX alternative":0.004176749981889291,
       "RELAX null":0.00397871921631754,
       "RELAX partitioned descriptive":0.004188079354984015,
       "k (general descriptive)":5.301456309232226,
       "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":6945.886057024934,
     "Log Likelihood":-3420.484282637879,
     "Rate Distributions":{
       "Shared":{
         "0":{
           "omega":2.201373594751134e-18,
           "proportion":0.5258178735075876
          },
         "1":{
           "omega":2.201373594751134e-18,
           "proportion":0.01992025780064184
          },
         "2":{
           "omega":2.201373412388544,
           "proportion":0.4542618686917706
          }
        }
      },
     "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":6909.668413948684,
     "Log Likelihood":-3408.69933855329,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0,
           "proportion":0.3825895192221547
          },
         "1":{
           "omega":0.003503464580598538,
           "proportion":0
          },
         "2":{
           "omega":2.417572962231385,
           "proportion":0.6174104807778453
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.2789425737851868,
           "rate":0.2834765074731829
          },
         "1":{
           "proportion":0.6311785441975573,
           "rate":0.9970973177052372
          },
         "2":{
           "proportion":0.089878882017256,
           "rate":3.244142488658602
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.3825895192221547
          },
         "1":{
           "omega":0.9998114377116485,
           "proportion":0
          },
         "2":{
           "omega":1.000029443594731,
           "proportion":0.6174104807778453
          }
        }
      },
     "display order":2,
     "estimated parameters":45
    },
   "RELAX null":{
     "AIC-c":6919.152853316747,
     "Log Likelihood":-3414.491495151524,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0,
           "proportion":0.3885051761591228
          },
         "1":{
           "omega":0.9958737025997172,
           "proportion":0
          },
         "2":{
           "omega":1.887643080900262,
           "proportion":0.6114948238408772
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.2642938080646302,
           "rate":0.2741590488311177
          },
         "1":{
           "proportion":0.633162055223991,
           "rate":0.9728788992663913
          },
         "2":{
           "proportion":0.1025441367113787,
           "rate":3.038218152856258
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.3885051761591228
          },
         "1":{
           "omega":0.9958737025997172,
           "proportion":0
          },
         "2":{
           "omega":1.887643080900262,
           "proportion":0.6114948238408772
          }
        }
      },
     "display order":3,
     "estimated parameters":44
    },
   "RELAX partitioned descriptive":{
     "AIC-c":6917.810941882631,
     "Log Likelihood":-3408.559317095162,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0.03550460650841439,
           "proportion":0.354985198548996
          },
         "1":{
           "omega":0.05439939847728128,
           "proportion":0.02231130867735708
          },
         "2":{
           "omega":2.333762420535514,
           "proportion":0.6227034927736469
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.3705590531463396
          },
         "1":{
           "omega":0,
           "proportion":0.06265340406614885
          },
         "2":{
           "omega":1.08372848194659,
           "proportion":0.5667875427875115
          }
        }
      },
     "display order":5,
     "estimated parameters":49
    }
  },
 "input":{
   "file name":"/tmp/tmpkgsdjj1d/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":"2.5.32",
 "test results":{
   "LRT":11.58431319646934,
   "p-value":0.0006651049394417186,
   "relaxation or intensification parameter":3.335337302186161e-05
  },
 "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":105
    },
   "Overall":{
     "order":0,
     "timer":3013
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":8
    },
   "RELAX alternative model fitting":{
     "order":3,
     "timer":1229
    },
   "RELAX null model fitting":{
     "order":4,
     "timer":690
    },
   "RELAX partitioned descriptive":{
     "order":5,
     "timer":980
    }
  }
}