view test-data/busted-out1.json @ 1:5c87e4907e08 draft

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

{
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   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.",
   "version":"1.2",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
   "authors":"Sergei L Kosakovsky Pond",
   "contact":"[e-mail]",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
  },
 "input":{
   "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.fa",
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   "number of sites":187,
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 "background":0,
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       "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
       "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
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 "Evidence Ratios":{
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   "optimized null":[
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    ]
  },
 "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":"busted.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,
       "MG94xREV with separate rates for branch sets":0,
       "unconstrained":0,
       "constrained":0
      },
     "Chimp":{
       "original name":"Chimp",
       "Nucleotide GTR":0.001818647577470898,
       "MG94xREV with separate rates for branch sets":0.001828142895085465,
       "unconstrained":0.001835079043904073,
       "constrained":0.001827227299324197
      },
     "Baboon":{
       "original name":"Baboon",
       "Nucleotide GTR":0.001683434956773037,
       "MG94xREV with separate rates for branch sets":0.001771624553208579,
       "unconstrained":0.001852571561323465,
       "constrained":0.001757260248005238
      },
     "RhMonkey":{
       "original name":"RhMonkey",
       "Nucleotide GTR":0.003773669075849421,
       "MG94xREV with separate rates for branch sets":0.003717699096857038,
       "unconstrained":0.003672835047422234,
       "constrained":0.00373144096412681
      },
     "Cow":{
       "original name":"Cow",
       "Nucleotide GTR":0.2483322373763571,
       "MG94xREV with separate rates for branch sets":0.2480141631033857,
       "unconstrained":0.2960120156157274,
       "constrained":0.2592686681333873
      },
     "Pig":{
       "original name":"Pig",
       "Nucleotide GTR":0.187244836750842,
       "MG94xREV with separate rates for branch sets":0.1926081878751187,
       "unconstrained":0.2187526946336905,
       "constrained":0.1943776301130502
      },
     "Horse":{
       "original name":"Horse",
       "Nucleotide GTR":0.2091766851769093,
       "MG94xREV with separate rates for branch sets":0.2111575880588217,
       "unconstrained":0.2572135566477119,
       "constrained":0.218486450878766
      },
     "Cat":{
       "original name":"Cat",
       "Nucleotide GTR":0.266381043956941,
       "MG94xREV with separate rates for branch sets":0.273601177885004,
       "unconstrained":0.3292215104251173,
       "constrained":0.28483085314287
      },
     "Mouse":{
       "original name":"Mouse",
       "Nucleotide GTR":0.1181831744338598,
       "MG94xREV with separate rates for branch sets":0.1201847378516324,
       "unconstrained":0.1489713993010398,
       "constrained":0.1233480139851019
      },
     "Rat":{
       "original name":"Rat",
       "Nucleotide GTR":0.06669700444436912,
       "MG94xREV with separate rates for branch sets":0.0670850471739789,
       "unconstrained":0.07366345007817726,
       "constrained":0.06713082546371778
      },
     "Node1":{
       "Nucleotide GTR":0.276880831396131,
       "MG94xREV with separate rates for branch sets":0.2843521449765504,
       "unconstrained":0.459085769955035,
       "constrained":0.3115534692518958
      },
     "Node12":{
       "Nucleotide GTR":0.01783434870161725,
       "MG94xREV with separate rates for branch sets":0.01788794906051452,
       "unconstrained":0.01828498503175797,
       "constrained":0.01770410398930177
      },
     "Node2":{
       "Nucleotide GTR":0.06617535490721377,
       "MG94xREV with separate rates for branch sets":0.06447679597474805,
       "unconstrained":0.0623969317369398,
       "constrained":0.06097949807503514
      },
     "Node3":{
       "Nucleotide GTR":0.09884524766349881,
       "MG94xREV with separate rates for branch sets":0.1017497956116402,
       "unconstrained":0.1285021744856729,
       "constrained":0.1065011238088613
      },
     "Node8":{
       "Nucleotide GTR":0.1061610073141143,
       "MG94xREV with separate rates for branch sets":0.1093806684969149,
       "unconstrained":0.1348034716617685,
       "constrained":0.1118205234697939
      },
     "Node9":{
       "Nucleotide GTR":0.02568007351415409,
       "MG94xREV with separate rates for branch sets":0.02593963430985144,
       "unconstrained":0.02761127562964508,
       "constrained":0.02639493109700932
      }
    },
   "attributes":{
     "original name":{
       "attribute type":"node label",
       "display order":0
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "unconstrained":{
       "attribute type":"branch length",
       "display order":0
      },
     "constrained":{
       "attribute type":"branch length",
       "display order":1
      }
    }
  },
 "test results":{
   "LRT":44.77492170961614,
   "p-value":1.893429857346973e-10
  }
}