annotate test-data/absrel-out1.json @ 0:bf97cacc1a55 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

{
 "analysis":{
   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
   "version":"2.0",
   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",
   "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"
  },
 "input":{
   "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_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":-3531.96369518556,
     "estimated parameters":24,
     "AIC-c":7112.577796875186,
     "Equilibrium frequencies":[
      [0.3563279857397504],
      [0.1837789661319073],
      [0.2402852049910873],
      [0.2196078431372549]
      ],
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
       "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
       "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
       "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
      },
     "display order":0
    },
   "Baseline MG94xREV":{
     "Log Likelihood":-3450.669934819203,
     "estimated parameters":46,
     "AIC-c":6995.711784065174,
     "Equilibrium frequencies":[
      [0.04787662253946073],
      [0.03913388100305117],
      [0.04844580322128512],
      [0.0407178971288476],
      [0.01817959331488358],
      [0.01485982100934833],
      [0.01839572120297191],
      [0.01546129971531724],
      [0.0190238172858878],
      [0.01554988139098808],
      [0.01924998172104109],
      [0.01617929156565557],
      [0.02798385246472159],
      [0.02287372613761008],
      [0.02831653817605838],
      [0.02379958245776909],
      [0.01680670574479072],
      [0.01373763619452979],
      [0.01700651207463693],
      [0.01429369239710176],
      [0.006381800954137531],
      [0.005216421415661322],
      [0.006457670922102578],
      [0.00542756570877943],
      [0.006678159032689796],
      [0.005458661598138652],
      [0.00675755225029668],
      [0.00567961101013393],
      [0.009823507779659469],
      [0.008029638769211124],
      [0.009940294440024354],
      [0.008354653231583485],
      [0.0329096029621651],
      [0.02689998621179963],
      [0.03330084840219455],
      [0.02798881284619018],
      [0.01249635346589736],
      [0.01021439657952951],
      [0.01264491622176376],
      [0.01062784315018763],
      [0.01307665913959002],
      [0.01068873273724336],
      [0.0132321208528494],
      [0.01112137894012831],
      [0.01923563996618058],
      [0.01572302316926395],
      [0.01946432265285621],
      [0.01635944157725275],
      [0.01977100255021048],
      [0.02057127040149398],
      [0.009184593415672956],
      [0.007507396443725858],
      [0.009293784349897772],
      [0.007811272183233558],
      [0.007856024926654371],
      [0.009725369116048951],
      [0.008174012048031599],
      [0.01413784690564137],
      [0.01155613719386138],
      [0.01430592453757226],
      [0.01202389319448819]
      ],
     "Rate Distributions":{
       "Per-branch omega":{
         "Mean":666666667.6064719,
         "Median":1.103169534345197,
         "2.5%":0,
         "97.5%":10000000000
        }
      },
     "display order":1
    },
   "Full adaptive model":{
     "Log Likelihood":-3414.992415597899,
     "estimated parameters":60,
     "AIC-c":6954.031265689993,
     "Rate Distributions":{
      },
     "display order":2
    }
  },
 "timers":{
   "Overall":{
     "timer":98,
     "order":0
    },
   "Preliminary model fitting":{
     "timer":0,
     "order":1
    },
   "Baseline model fitting":{
     "timer":1,
     "order":2
    },
   "Complexity analysis":{
     "timer":36,
     "order":3
    },
   "Full adaptive model fitting":{
     "timer":8,
     "order":4
    },
   "Testing for selection":{
     "timer":53,
     "order":5
    }
  },
 "test results":{
   "P-value threshold":0.05,
   "tested":16,
   "positive test results":3
  },
 "tested":{
   "0":{
     "Pig":"test",
     "Cow":"test",
     "Node3":"test",
     "Horse":"test",
     "Cat":"test",
     "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":"absrel.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,
       "Baseline MG94xREV":0,
       "Baseline MG94xREV omega ratio":1,
       "Rate classes":1,
       "Full adaptive model":0,
       "Rate Distributions":[
        [1, 1]
        ],
       "LRT":0,
       "Uncorrected P-value":1,
       "Corrected P-value":1
      },
     "Chimp":{
       "original name":"Chimp",
       "Nucleotide GTR":0.001818174796225333,
       "Baseline MG94xREV":0.001839770270131542,
       "Baseline MG94xREV omega ratio":10000000000,
       "Rate classes":1,
       "Full adaptive model":0.001845806111200226,
       "Rate Distributions":[
        [10000000000, 1]
        ],
       "LRT":0.6362875427803374,
       "Uncorrected P-value":0.303261123771571,
       "Corrected P-value":1
      },
     "Baboon":{
       "original name":"Baboon",
       "Nucleotide GTR":0.001682034724848474,
       "Baseline MG94xREV":0.001821072110941238,
       "Baseline MG94xREV omega ratio":0,
       "Rate classes":1,
       "Full adaptive model":0.001808294153407354,
       "Rate Distributions":[
        [0, 1]
        ],
       "LRT":0,
       "Uncorrected P-value":1,
       "Corrected P-value":1
      },
     "RhMonkey":{
       "original name":"RhMonkey",
       "Nucleotide GTR":0.003775509884015639,
       "Baseline MG94xREV":0.003671340584166445,
       "Baseline MG94xREV omega ratio":10000000000,
       "Rate classes":1,
       "Full adaptive model":0.003682180830540259,
       "Rate Distributions":[
        [10000000000, 1]
        ],
       "LRT":1.200615147074132,
       "Uncorrected P-value":0.2192326116145807,
       "Corrected P-value":1
      },
     "Cow":{
       "original name":"Cow",
       "Nucleotide GTR":0.248257545271419,
       "Baseline MG94xREV":0.2535517510207829,
       "Baseline MG94xREV omega ratio":1.957039676836281,
       "Rate classes":2,
       "Full adaptive model":0.3959632497370367,
       "Rate Distributions":[
        [0, 0.5384412409742189],
        [10.58123012791267, 0.4615587590257811]
        ],
       "LRT":24.50128746473001,
       "Uncorrected P-value":1.583131814197891e-06,
       "Corrected P-value":2.533010902716626e-05
      },
     "Pig":{
       "original name":"Pig",
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       "Baseline MG94xREV":0.1913752025483544,
       "Baseline MG94xREV omega ratio":1.354835319497051,
       "Rate classes":1,
       "Full adaptive model":0.1823079562415392,
       "Rate Distributions":[
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        ],
       "LRT":0.5083013304356427,
       "Uncorrected P-value":0.3278475069550038,
       "Corrected P-value":1
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     "Horse":{
       "original name":"Horse",
       "Nucleotide GTR":0.2092211101976542,
       "Baseline MG94xREV":0.2093433205074538,
       "Baseline MG94xREV omega ratio":1.262933703792719,
       "Rate classes":2,
       "Full adaptive model":0.2696870893488891,
       "Rate Distributions":[
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        ],
       "LRT":9.839972152766677,
       "Uncorrected P-value":0.002531289908698275,
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      },
     "Cat":{
       "original name":"Cat",
       "Nucleotide GTR":0.2662269345134692,
       "Baseline MG94xREV":0.2773733494290757,
       "Baseline MG94xREV omega ratio":1.619113019542315,
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       "Rate Distributions":[
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       "LRT":13.05292728184577,
       "Uncorrected P-value":0.000499814517576469,
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      },
     "Mouse":{
       "original name":"Mouse",
       "Nucleotide GTR":0.1181551390736968,
       "Baseline MG94xREV":0.1220127721537473,
       "Baseline MG94xREV omega ratio":0.5307054960008202,
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       "Rate Distributions":[
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       "Uncorrected P-value":1,
       "Corrected P-value":1
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     "Rat":{
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       "Nucleotide GTR":0.06673994656462794,
       "Baseline MG94xREV":0.06546903135094065,
       "Baseline MG94xREV omega ratio":1.103169534345197,
       "Rate classes":1,
       "Full adaptive model":0.06894368446818594,
       "Rate Distributions":[
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        ],
       "LRT":0.04180897168953379,
       "Uncorrected P-value":0.4613906175252571,
       "Corrected P-value":1
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     "Node1":{
       "Nucleotide GTR":0.2772613398768408,
       "Baseline MG94xREV":0.2903229694372956,
       "Baseline MG94xREV omega ratio":0.4389914526526448,
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       "Full adaptive model":0.3664538683295676,
       "Rate Distributions":[
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       "LRT":1.095302853601424,
       "Uncorrected P-value":0.232551772988317,
       "Corrected P-value":1
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     "Node12":{
       "Nucleotide GTR":0.01783922546179193,
       "Baseline MG94xREV":0.01797212760838867,
       "Baseline MG94xREV omega ratio":0.3712490894908597,
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       "Full adaptive model":0.01648897148329989,
       "Rate Distributions":[
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       "LRT":0,
       "Uncorrected P-value":1,
       "Corrected P-value":1
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     "Node2":{
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       "Baseline MG94xREV":0.06580724801157116,
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       "Full adaptive model":0.1259563484776556,
       "Rate Distributions":[
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       "Uncorrected P-value":0.007599562698001494,
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       "LRT":6.598417720076213,
       "Uncorrected P-value":0.0131150962965953,
       "Corrected P-value":0.1442660592625483
      },
     "Node8":{
       "Nucleotide GTR":0.1061134663636472,
       "Baseline MG94xREV":0.110140333084973,
       "Baseline MG94xREV omega ratio":1.896243438714738,
       "Rate classes":2,
       "Full adaptive model":0.2165540926910564,
       "Rate Distributions":[
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       "LRT":7.97288393366216,
       "Uncorrected P-value":0.006519360772582139,
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     "Node9":{
       "Nucleotide GTR":0.02566719422260768,
       "Baseline MG94xREV":0.02590165433349057,
       "Baseline MG94xREV omega ratio":0.4071738826525522,
       "Rate classes":1,
       "Full adaptive model":0.02766629863085238,
       "Rate Distributions":[
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        ],
       "LRT":0,
       "Uncorrected P-value":1,
       "Corrected P-value":1
      }
    },
   "attributes":{
     "original name":{
       "attribute type":"node label",
       "display order":-1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "Baseline MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Baseline MG94xREV omega ratio":{
       "attribute type":"branch label",
       "display order":1
      },
     "Rate classes":{
       "attribute type":"branch label",
       "display order":2
      },
     "Full adaptive model":{
       "attribute type":"branch length",
       "display order":2
      },
     "Rate Distributions":{
       "attribute type":"branch label",
       "display order":3
      },
     "LRT":{
       "attribute type":"branch label",
       "display order":4
      },
     "Uncorrected P-value":{
       "attribute type":"branch label",
       "display order":5
      },
     "Corrected P-value":{
       "attribute type":"branch label",
       "display order":6
      }
    }
  }
}