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

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

{
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
   "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. v2.2 adds support for multiple-hit models",
   "contact":"[e-mail]",
   "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.",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"2.2"
  },
 "branch attributes":{
   "0":{
     "Baboon":{
       "Baseline MG94xREV":0.001816807585564731,
       "Baseline MG94xREV omega ratio":0,
       "Corrected P-value":1,
       "Full adaptive model":0.001810407118394509,
       "LRT":0,
       "Nucleotide GTR":0.001678881906620672,
       "Rate Distributions":        [
[0, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "original name":"Baboon",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      },
     "Cat":{
       "Baseline MG94xREV":0.2286001363527903,
       "Baseline MG94xREV omega ratio":1.403298474422089,
       "Corrected P-value":1,
       "Full adaptive model":0.1219386838393392,
       "LRT":1.644967676056694,
       "Nucleotide GTR":0.265904547400163,
       "Rate Distributions":        [
[0.2130519766306851, 0.6352283641519592],
        [2.628217450705319, 0.3647716358480408] 
        ],
       "Rate classes":2,
       "Uncorrected P-value":0.171730764045231,
       "original name":"Cat",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      },
     "Chimp":{
       "Baseline MG94xREV":0.001840311209746262,
       "Baseline MG94xREV omega ratio":10000000000,
       "Corrected P-value":1,
       "Full adaptive model":0.001841979303044237,
       "LRT":0.6159123786974305,
       "Nucleotide GTR":0.001816713800925801,
       "Rate Distributions":        [
[10000000000, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":0.3069983227523322,
       "original name":"Chimp",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      },
     "Cow":{
       "Baseline MG94xREV":0.2070244948790512,
       "Baseline MG94xREV omega ratio":2.153434974462683,
       "Corrected P-value":0.5006146299996015,
       "Full adaptive model":0.1241125417707662,
       "LRT":4.898194538953248,
       "Nucleotide GTR":0.2481512612523618,
       "Rate Distributions":        [
[0, 0.52318726440949],
        [2.444056517734385, 0.47681273559051] 
        ],
       "Rate classes":2,
       "Uncorrected P-value":0.03128841437497509,
       "original name":"Cow",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      },
     "Horse":{
       "Baseline MG94xREV":0.190365915457708,
       "Baseline MG94xREV omega ratio":1.182933895494305,
       "Corrected P-value":1,
       "Full adaptive model":0.0869489794025302,
       "LRT":2.047309801283518,
       "Nucleotide GTR":0.2090927256979082,
       "Rate Distributions":        [
[0, 0.5397658078247131],
        [1.633257246666139, 0.4602341921752869] 
        ],
       "Rate classes":2,
       "Uncorrected P-value":0.1382789032066179,
       "original name":"Horse",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      },
     "Human":{
       "Baseline MG94xREV":0,
       "Baseline MG94xREV omega ratio":1,
       "Corrected P-value":1,
       "Full adaptive model":0,
       "LRT":0,
       "Nucleotide GTR":0,
       "Rate Distributions":        [
[1, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "original name":"Human",
       "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574
      },
     "Mouse":{
       "Baseline MG94xREV":0.1083167307250788,
       "Baseline MG94xREV omega ratio":0.5108576904540283,
       "Corrected P-value":1,
       "Full adaptive model":0.1078010043714489,
       "LRT":0,
       "Nucleotide GTR":0.1181001275359051,
       "Rate Distributions":        [
[0.5087375113796073, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "original name":"Mouse",
       "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548
      },
     "Node1":{
       "Baseline MG94xREV":0.2542393300501047,
       "Baseline MG94xREV omega ratio":0.2997498382776075,
       "Corrected P-value":1,
       "Full adaptive model":0.2550466752020236,
       "LRT":0,
       "Nucleotide GTR":0.2767426965701868,
       "Rate Distributions":        [
[0.2932817609633239, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921
      },
     "Node12":{
       "Baseline MG94xREV":0.01400815185374474,
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       "Corrected P-value":1,
       "Full adaptive model":0.01437973904273591,
       "LRT":0,
       "Nucleotide GTR":0.01784721909304638,
       "Rate Distributions":        [
[0.3037614070859027, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814
      },
     "Node2":{
       "Baseline MG94xREV":0.0400106272595141,
       "Baseline MG94xREV omega ratio":0.116408812566168,
       "Corrected P-value":1,
       "Full adaptive model":0.03991940069030483,
       "LRT":0,
       "Nucleotide GTR":0.06613304839358287,
       "Rate Distributions":        [
[0.1193993042178124, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
      },
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       "Baseline MG94xREV":0.08548068002443369,
       "Baseline MG94xREV omega ratio":1.293385437932658,
       "Corrected P-value":1,
       "Full adaptive model":0.08590119038008139,
       "LRT":0.1383887036890883,
       "Nucleotide GTR":0.09881178513658169,
       "Rate Distributions":        [
[1.330576641567385, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":0.4219212196398351,
       "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
      },
     "Node8":{
       "Baseline MG94xREV":0.09463393920061362,
       "Baseline MG94xREV omega ratio":1.862136443854597,
       "Corrected P-value":1,
       "Full adaptive model":0.0958035263641453,
       "LRT":0.7150293976401372,
       "Nucleotide GTR":0.1062333225692588,
       "Rate Distributions":        [
[1.883870769808856, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":0.2893795680778183,
       "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092
      },
     "Node9":{
       "Baseline MG94xREV":0.02846111726225027,
       "Baseline MG94xREV omega ratio":0.4321055128385307,
       "Corrected P-value":1,
       "Full adaptive model":0.02810856974543091,
       "LRT":0,
       "Nucleotide GTR":0.02566185438854229,
       "Rate Distributions":        [
[0.4185836885800617, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      },
     "Pig":{
       "Baseline MG94xREV":0.1782835053555321,
       "Baseline MG94xREV omega ratio":1.275728452678247,
       "Corrected P-value":1,
       "Full adaptive model":0.1729188354138871,
       "LRT":0.3324036585026988,
       "Nucleotide GTR":0.1871760137183495,
       "Rate Distributions":        [
[1.235108129487059, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":0.3669120164240152,
       "original name":"Pig",
       "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695
      },
     "Rat":{
       "Baseline MG94xREV":0.06315403896300904,
       "Baseline MG94xREV omega ratio":0.8744850915248316,
       "Corrected P-value":1,
       "Full adaptive model":0.06408078523886611,
       "LRT":0,
       "Nucleotide GTR":0.0666364425850592,
       "Rate Distributions":        [
[0.8782045320352186, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":1,
       "original name":"Rat",
       "rate at which 2 nucleotides are changed instantly within a single codon":0.1346164190615118
      },
     "RhMonkey":{
       "Baseline MG94xREV":0.003671939837747083,
       "Baseline MG94xREV omega ratio":10000000000,
       "Corrected P-value":1,
       "Full adaptive model":0.003675047654636179,
       "LRT":1.165062770327495,
       "Nucleotide GTR":0.003777016173741061,
       "Rate Distributions":        [
[10000000000, 1] 
        ],
       "Rate classes":1,
       "Uncorrected P-value":0.2236284592802686,
       "original name":"RhMonkey",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
      }
    },
   "attributes":{
     "Baseline MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Baseline MG94xREV omega ratio":{
       "attribute type":"branch label",
       "display order":1
      },
     "Corrected P-value":{
       "attribute type":"branch label",
       "display order":6
      },
     "Full adaptive model":{
       "attribute type":"branch length",
       "display order":2
      },
     "LRT":{
       "attribute type":"branch label",
       "display order":4
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "Rate Distributions":{
       "attribute type":"branch label",
       "display order":3
      },
     "Rate classes":{
       "attribute type":"branch label",
       "display order":2
      },
     "Uncorrected P-value":{
       "attribute type":"branch label",
       "display order":5
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      },
     "rate at which 2 nucleotides are changed instantly within a single codon":{
       "attribute type":"branch label",
       "display order":7
      }
    }
  },
 "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":"absrel.filter.default"
    }
  },
 "fits":{
   "Baseline MG94xREV":{
     "AIC-c":6983.763305606333,
     "Equilibrium frequencies":      [
[0.04875339327772683],
      [0.03982858547830345],
      [0.04946803524790992],
      [0.04152216138298744],
      [0.01811683453600613],
      [0.01480036248560469],
      [0.0183823965708893],
      [0.01542969784826435],
      [0.01894694796506697],
      [0.01547851515238824],
      [0.01922467805342367],
      [0.01613668666381816],
      [0.02832099415740372],
      [0.02313654621336914],
      [0.02873613184734657],
      [0.02412034959764736],
      [0.01662182431200483],
      [0.01357902918971745],
      [0.01686547203528639],
      [0.01415643148428886],
      [0.006176695005242439],
      [0.005045987744654046],
      [0.006267234867003878],
      [0.005260551308914496],
      [0.006459711194459957],
      [0.005277194922783805],
      [0.006554399593040238],
      [0.005501589790395056],
      [0.009655668202293983],
      [0.007888099278638223],
      [0.009797203904398108],
      [0.008223514024394991],
      [0.03326722643528176],
      [0.02717732003095303],
      [0.03375486749252685],
      [0.02833294365668738],
      [0.01236215156074466],
      [0.01009913314808799],
      [0.01254335971371867],
      [0.01052856463184265],
      [0.01292858539344675],
      [0.0105618754683007],
      [0.0131180965046964],
      [0.01101098350431497],
      [0.0193250328267319],
      [0.01578738770911659],
      [0.0196083049972345],
      [0.01645869298147252],
      [0.01962343746171723],
      [0.02045785777700414],
      [0.008926115885166477],
      [0.007292098982657142],
      [0.009056957588961733],
      [0.007602170831388156],
      [0.007626222986467745],
      [0.009471947420992787],
      [0.007950502328516303],
      [0.01395367801862353],
      [0.01139931439306339],
      [0.01415821524731906],
      [0.01188403168729233] 
      ],
     "Log Likelihood":-3427.720059001285,
     "Rate Distributions":{
       "Per-branch delta":{
         "2.5%":0,
         "97.5%":12.07373117808175,
         "Mean":1.277646334033236,
         "Median":0.4551223038316586
        },
       "Per-branch omega":{
         "2.5%":0,
         "97.5%":2.153434974462683,
         "Mean":666666667.5119981,
         "Median":1
        }
      },
     "display order":1,
     "estimated parameters":62
    },
   "Full adaptive model":{
     "AIC-c":6972.859938351839,
     "Log Likelihood":-3415.824749853321,
     "Rate Distributions":{
      },
     "display order":2,
     "estimated parameters":68
    },
   "Nucleotide GTR":{
     "AIC-c":7112.857317645923,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "Log Likelihood":-3532.321228205235,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,
       "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,
       "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,
       "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399
      },
     "display order":0,
     "estimated parameters":24
    }
  },
 "input":{
   "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
   "number of sequences":10,
   "number of sites":187,
   "partition count":1,
   "trees":{
     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,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":{
   "P-value threshold":0.05,
   "positive test results":0,
   "tested":16
  },
 "tested":{
   "0":{
     "Baboon":"test",
     "Cat":"test",
     "Chimp":"test",
     "Cow":"test",
     "Horse":"test",
     "Human":"test",
     "Mouse":"test",
     "Node1":"test",
     "Node12":"test",
     "Node2":"test",
     "Node3":"test",
     "Node8":"test",
     "Node9":"test",
     "Pig":"test",
     "Rat":"test",
     "RhMonkey":"test"
    }
  },
 "timers":{
   "Baseline model fitting":{
     "order":2,
     "timer":17
    },
   "Complexity analysis":{
     "order":3,
     "timer":110
    },
   "Full adaptive model fitting":{
     "order":4,
     "timer":20
    },
   "Overall":{
     "order":0,
     "timer":259
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":0
    },
   "Testing for selection":{
     "order":5,
     "timer":112
    }
  }
}