annotate test-data/relax-out1.json @ 29:d0f087aae1a3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"

{
 "analysis":0,
 "branch attributes":{
   "0":{
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       "General descriptive":0.001858767762813579,
       "MG94xREV with separate rates for branch sets":0.001769472024099301,
       "Nucleotide GTR":0.001680040630127455,
       "RELAX alternative":0.001872256662230973,
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       "RELAX partitioned descriptive":0.001898170574782418,
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       "original name":"Baboon"
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     "Cat":{
       "General descriptive":0.3644803308678196,
       "MG94xREV with separate rates for branch sets":0.2796030091674721,
       "Nucleotide GTR":0.2660909938917123,
       "RELAX alternative":0.3689219388980864,
       "RELAX null":0.3256077554105627,
       "RELAX partitioned descriptive":0.3717219559832593,
       "k (general descriptive)":2.314507643873676,
       "original name":"Cat"
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     "Chimp":{
       "General descriptive":0.001848680051431209,
       "MG94xREV with separate rates for branch sets":0.001825434296531533,
       "Nucleotide GTR":0.001818373670119325,
       "RELAX alternative":0.001831703934281931,
       "RELAX null":0.00183525802483954,
       "RELAX partitioned descriptive":0.001832717232153088,
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       "original name":"Chimp"
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     "Cow":{
       "General descriptive":0.3733627618450006,
       "MG94xREV with separate rates for branch sets":0.2520490246808783,
       "Nucleotide GTR":0.2481025999892287,
       "RELAX alternative":0.342739998512865,
       "RELAX null":0.2948256709356563,
       "RELAX partitioned descriptive":0.3466331923230422,
       "k (general descriptive)":2.846155982935764,
       "original name":"Cow"
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     "Horse":{
       "General descriptive":0.2802176313870697,
       "MG94xREV with separate rates for branch sets":0.2158304510870495,
       "Nucleotide GTR":0.2090310577070883,
       "RELAX alternative":0.3058487498567987,
       "RELAX null":0.2559911331878715,
       "RELAX partitioned descriptive":0.3034694616209482,
       "k (general descriptive)":1.926646959057857,
       "original name":"Horse"
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     "Human":{
       "General descriptive":0,
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":0,
       "RELAX alternative":0,
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       "RELAX partitioned descriptive":0,
       "k (general descriptive)":1.462532487172471,
       "original name":"Human"
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     "Mouse":{
       "General descriptive":0.1307950021191255,
       "MG94xREV with separate rates for branch sets":0.1197727080219867,
       "Nucleotide GTR":0.1180171198334285,
       "RELAX alternative":0.1346501492117481,
       "RELAX null":0.1468861666244963,
       "RELAX partitioned descriptive":0.1475623398849678,
       "k (general descriptive)":0.4639609139295889,
       "original name":"Mouse"
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     "Node1":{
       "General descriptive":0.350050900813081,
       "MG94xREV with separate rates for branch sets":0.2857356440257563,
       "Nucleotide GTR":0.2767237570684924,
       "RELAX alternative":0.3856490868629754,
       "RELAX null":0.4521046025119397,
       "RELAX partitioned descriptive":0.4358952685746469,
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     "Node12":{
       "General descriptive":0.01766384491594095,
       "MG94xREV with separate rates for branch sets":0.01800001211221997,
       "Nucleotide GTR":0.01784803874223016,
       "RELAX alternative":0.01835132674304535,
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       "RELAX partitioned descriptive":0.01878351896299688,
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     "Node2":{
       "General descriptive":0.05771641706257456,
       "MG94xREV with separate rates for branch sets":0.06169547093990335,
       "Nucleotide GTR":0.06613162123865737,
       "RELAX alternative":0.05450381496370671,
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     "Node3":{
       "General descriptive":0.133048972566238,
       "MG94xREV with separate rates for branch sets":0.09736816312927643,
       "Nucleotide GTR":0.09886326330774685,
       "RELAX alternative":0.1168284793254293,
       "RELAX null":0.1276889506286756,
       "RELAX partitioned descriptive":0.1195376339442456,
       "k (general descriptive)":1.980345386854111
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     "Node8":{
       "General descriptive":0.1404364853762839,
       "MG94xREV with separate rates for branch sets":0.1092041281639667,
       "Nucleotide GTR":0.106239268140425,
       "RELAX alternative":0.1283918913740865,
       "RELAX null":0.1343238120118072,
       "RELAX partitioned descriptive":0.1363833239244288,
       "k (general descriptive)":2.210166852936262
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     "Node9":{
       "General descriptive":0.02665050120918479,
       "MG94xREV with separate rates for branch sets":0.02578196090462333,
       "Nucleotide GTR":0.02566573875750134,
       "RELAX alternative":0.02679622227446188,
       "RELAX null":0.02754241929890747,
       "RELAX partitioned descriptive":0.0274479920792393,
       "k (general descriptive)":0.0733131770696667
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     "Pig":{
       "General descriptive":0.2104601216238473,
       "MG94xREV with separate rates for branch sets":0.1902977811335351,
       "Nucleotide GTR":0.1871893456388788,
       "RELAX alternative":0.19752905148822,
       "RELAX null":0.2165309177979844,
       "RELAX partitioned descriptive":0.2074828949843082,
       "k (general descriptive)":1.577441472516679,
       "original name":"Pig"
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     "Rat":{
       "General descriptive":0.07164210204456434,
       "MG94xREV with separate rates for branch sets":0.06709541225974219,
       "Nucleotide GTR":0.06661283005976348,
       "RELAX alternative":0.07247047023746757,
       "RELAX null":0.07343093575256582,
       "RELAX partitioned descriptive":0.07560655472076994,
       "k (general descriptive)":1.318174884032695,
       "original name":"Rat"
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     "RhMonkey":{
       "General descriptive":0.003674505194636419,
       "MG94xREV with separate rates for branch sets":0.003716165486244973,
       "Nucleotide GTR":0.003775170135617877,
       "RELAX alternative":0.003636176595806718,
       "RELAX null":0.003665938723426083,
       "RELAX partitioned descriptive":0.003624376345656283,
       "k (general descriptive)":5.171610533872274,
       "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",
       "display order":0
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     "RELAX alternative":{
       "attribute type":"branch length",
       "display order":2
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     "RELAX null":{
       "attribute type":"branch length",
       "display order":3
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     "RELAX partitioned descriptive":{
       "attribute type":"branch length",
       "display order":5
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     "k (general descriptive)":{
       "attribute type":"branch label",
       "display order":4
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     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
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 "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":6945.891353881681,
     "Log Likelihood":-3420.486931066253,
     "Rate Distributions":{
       "Shared":{
         "0":{
           "omega":2.202835393423959e-18,
           "proportion":0.4487473029633234
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         "1":{
           "omega":2.202835393423959e-18,
           "proportion":0.09729227592412616
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         "2":{
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           "proportion":0.4539604211125504
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     "display order":4,
     "estimated parameters":51
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6987.565999172035,
     "Equilibrium frequencies":      [
[0.04876086397632926],
      [0.03982224127745371],
      [0.0494959405650269],
      [0.04152830682371345],
      [0.01810345074594235],
      [0.01478480742075003],
      [0.01837636270304883],
      [0.01541821854326533],
      [0.01892910005547028],
      [0.01545910240515689],
      [0.01921445878706794],
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      [0.02829747763884322],
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      [0.02410019507229243],
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      [0.006177213955434187],
      [0.005044834822351987],
      [0.006270336287397383],
      [0.00526096577332031],
      [0.006458939937330408],
      [0.005274916061901906],
      [0.006556309326397028],
      [0.005500904159606446],
      [0.009655594186286731],
      [0.007885574003572761],
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      [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":-3461.208149286616,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *Reference*":        [
[0.7682335289209781, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *Test*":        [
[1.605439824256426, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":32
    },
   "Nucleotide GTR":{
     "AIC-c":7112.857310169033,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "Log Likelihood":-3532.32122446679,
     "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":0.2647746107611847,
       "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
       "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
       "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
      },
     "display order":0,
     "estimated parameters":24
    },
   "RELAX alternative":{
     "AIC-c":6931.922980697387,
     "Log Likelihood":-3429.234812770952,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":1.762268314739328e-19,
           "proportion":0.4504132080156107
          },
         "1":{
           "omega":1.762268314739328e-19,
           "proportion":0.08749553114962015
          },
         "2":{
           "omega":2.19971015101232,
           "proportion":0.4620912608347691
          }
        },
       "Test":{
         "0":{
           "omega":1.054840660215593e-44,
           "proportion":0.4504132080156107
          },
         "1":{
           "omega":1.054840660215593e-44,
           "proportion":0.08749553114962015
          },
         "2":{
           "omega":6.350765030542244,
           "proportion":0.4620912608347691
          }
        }
      },
     "display order":2,
     "estimated parameters":36
    },
   "RELAX null":{
     "AIC-c":6946.046672507471,
     "Log Likelihood":-3437.336313352972,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0.1150006822953211,
           "proportion":0.542405144031307
          },
         "1":{
           "omega":0.2401508033814633,
           "proportion":0.08223353569636478
          },
         "2":{
           "omega":3.69263720947284,
           "proportion":0.3753613202723282
          }
        },
       "Test":{
         "0":{
           "omega":0.1150006822953211,
           "proportion":0.542405144031307
          },
         "1":{
           "omega":0.2401508033814633,
           "proportion":0.08223353569636478
          },
         "2":{
           "omega":3.69263720947284,
           "proportion":0.3753613202723282
          }
        }
      },
     "display order":3,
     "estimated parameters":35
    },
   "RELAX partitioned descriptive":{
     "AIC-c":6937.04707353565,
     "Log Likelihood":-3427.626871923648,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0.1943306885168281,
           "proportion":0.3359458135547653
          },
         "1":{
           "omega":0.2607558478587815,
           "proportion":0.4332550437039296
          },
         "2":{
           "omega":4.134271224300374,
           "proportion":0.2307991427413052
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.4753488415962343
          },
         "1":{
           "omega":0,
           "proportion":0.03858318603767072
          },
         "2":{
           "omega":6.017221959238516,
           "proportion":0.486067972366095
          }
        }
      },
     "display order":5,
     "estimated parameters":40
    }
  },
 "input":{
   "file name":"/tmp/tmpbauyxvdv/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)"
    }
  },
 "test results":{
   "LRT":16.20300116404087,
   "p-value":5.690389451429301e-05,
   "relaxation or intensification parameter":2.344938789085876
  },
 "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":132
    },
   "Overall":{
     "order":0,
     "timer":324
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":8
    },
   "RELAX alternative model fitting":{
     "order":3,
     "timer":65
    },
   "RELAX null model fitting":{
     "order":4,
     "timer":66
    },
   "RELAX partitioned descriptive":{
     "order":5,
     "timer":53
    }
  }
}