annotate test-data/busted-out2-1.json @ 5:11dd1a96ffe9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"

{
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    ]
  },
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
   "contact":"[e-mail]",
   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "version":"3.1"
  },
 "background":1,
 "branch attributes":{
   "0":{
     "B_FR_83_HXB2":{
       "MG94xREV with separate rates for branch sets":0.0124534911696585,
       "Nucleotide GTR":0.01178680392701259,
       "constrained":0.0133332678009897,
       "original name":"B_FR_83_HXB2",
       "unconstrained":0.01333097793183841
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     "B_US_83_RF":{
       "MG94xREV with separate rates for branch sets":0.02861194347570897,
       "Nucleotide GTR":0.02637179869727959,
       "constrained":0.03221962988361129,
       "original name":"B_US_83_RF",
       "unconstrained":0.03256468480049571
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     "B_US_86_JRFL":{
       "MG94xREV with separate rates for branch sets":0.01907096200225401,
       "Nucleotide GTR":0.01766254318226218,
       "constrained":0.0202680273768515,
       "original name":"B_US_86_JRFL",
       "unconstrained":0.02050998211592096
      },
     "B_US_90_WEAU160":{
       "MG94xREV with separate rates for branch sets":0.0228124185259555,
       "Nucleotide GTR":0.0208836028381146,
       "constrained":0.02350080060535386,
       "original name":"B_US_90_WEAU160",
       "unconstrained":0.03169576721730974
      },
     "D_CD_83_ELI":{
       "MG94xREV with separate rates for branch sets":0.02096580136021227,
       "Nucleotide GTR":0.01905599613120992,
       "constrained":0.02146725583386667,
       "original name":"D_CD_83_ELI",
       "unconstrained":0.02163106296740794
      },
     "D_CD_83_NDK":{
       "MG94xREV with separate rates for branch sets":0.01029979658511127,
       "Nucleotide GTR":0.009776698714183414,
       "constrained":0.01035332290986223,
       "original name":"D_CD_83_NDK",
       "unconstrained":0.01033266120816073
      },
     "D_CD_84_84ZR085":{
       "MG94xREV with separate rates for branch sets":0.0311654066957857,
       "Nucleotide GTR":0.02822254903672137,
       "constrained":0.03323755030380494,
       "original name":"D_CD_84_84ZR085",
       "unconstrained":0.03361093648063813
      },
     "D_UG_94_94UG114":{
       "MG94xREV with separate rates for branch sets":0.05961647055090802,
       "Nucleotide GTR":0.05323070232023583,
       "constrained":0.06686538335493719,
       "original name":"D_UG_94_94UG114",
       "unconstrained":0.06754551106553502
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     "Node1":{
       "MG94xREV with separate rates for branch sets":0.02629484580500255,
       "Nucleotide GTR":0.02355240508560319,
       "constrained":0.02886080451868769,
       "unconstrained":0.02913820563215103
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     "Node10":{
       "MG94xREV with separate rates for branch sets":0.001918758877996093,
       "Nucleotide GTR":0.002230248981703367,
       "constrained":0.001805007516719466,
       "unconstrained":0.001821173275343402
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     "Node2":{
       "MG94xREV with separate rates for branch sets":0.003971092177388864,
       "Nucleotide GTR":0.003949360371801276,
       "constrained":0.002472638754288051,
       "unconstrained":0.002387715711685514
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     "Node3":{
       "MG94xREV with separate rates for branch sets":0.01135514370835145,
       "Nucleotide GTR":0.01048442975058683,
       "constrained":0.01356000749275525,
       "unconstrained":0.01374972129226249
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     "Node9":{
       "MG94xREV with separate rates for branch sets":0.005568732807049801,
       "Nucleotide GTR":0.004986123424162501,
       "constrained":0.00559084970119209,
       "unconstrained":0.005669013080318036
      }
    },
   "attributes":{
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "constrained":{
       "attribute type":"branch length",
       "display order":1
      },
     "original name":{
       "attribute type":"node label",
       "display order":0
      },
     "unconstrained":{
       "attribute type":"branch length",
       "display order":0
      }
    }
  },
 "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, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439] 
      ],
     "name":"busted.filter.default"
    }
  },
 "fits":{
   "Constrained model":{
     "AIC-c":6401.571605880178,
     "Log Likelihood":-3164.403373999521,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":0.1702532607798455,
           "proportion":0.8127334552706815
          },
         "1":{
           "omega":0.2017838473060485,
           "proportion":0.1774848965120759
          },
         "2":{
           "omega":13.15236788524238,
           "proportion":0.00978164821724258
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.8358903801628909
          },
         "1":{
           "omega":1,
           "proportion":0.1436055877954064
          },
         "2":{
           "omega":1,
           "proportion":0.02050403204170275
          }
        }
      },
     "display order":3,
     "estimated parameters":36
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6410.490466219016,
     "Equilibrium frequencies":      [
[0.07535940345366139],
      [0.01443006409728228],
      [0.02915821068672351],
      [0.02954870567752823],
      [0.03219408024958758],
      [0.006164627375802654],
      [0.01245659774045292],
      [0.01262342001471309],
      [0.0276793164843978],
      [0.005300125700761717],
      [0.01070973633984303],
      [0.01085316415297191],
      [0.0418125103783387],
      [0.008006395714089126],
      [0.01617817990958604],
      [0.0163948426631036],
      [0.0409913146415633],
      [0.007849150478922548],
      [0.01586044121725868],
      [0.01607284872448998],
      [0.01751178502783737],
      [0.003353213651232053],
      [0.006775694789785172],
      [0.006866436807635995],
      [0.01505600521072376],
      [0.002882972930821469],
      [0.005825499564956559],
      [0.005903516300053625],
      [0.02274367484777162],
      [0.004355032959661065],
      [0.008800028033786655],
      [0.008917880494044083],
      [0.06143704799998004],
      [0.01176416611541591],
      [0.0237713451467977],
      [0.0240896977132239],
      [0.0262463496652457],
      [0.005025736545566795],
      [0.01015528996016046],
      [0.01029129247081581],
      [0.02256567087217255],
      [0.004320948178469224],
      [0.008731154380523415],
      [0.00884808446536876],
      [0.034087812394816],
      [0.006527245376826684],
      [0.01318932435908579],
      [0.01336595951511979],
      [0.01178447449308153],
      [0.02413128354890585],
      [0.0262916585104385],
      [0.005034412430862358],
      [0.01017282094890981],
      [0.01030905823951665],
      [0.004328407393735399],
      [0.008746226896405704],
      [0.008863358836639712],
      [0.03414665788893068],
      [0.006538513303760755],
      [0.0132120929750345],
      [0.01338903305480236] 
      ],
     "Log Likelihood":-3175.995949441886,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.2379324068936849, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.1777604776475358, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":29
    },
   "Nucleotide GTR":{
     "AIC-c":6683.094244259512,
     "Equilibrium frequencies":      [
[0.4044507575757576],
      [0.1662878787878788],
      [0.2095643939393939],
      [0.2196969696969697] 
      ],
     "Log Likelihood":-3320.503280793639,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,
       "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,
       "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,
       "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568
      },
     "display order":0,
     "estimated parameters":21
    },
   "Unconstrained model":{
     "AIC-c":6400.149223170942,
     "Log Likelihood":-3162.670820660715,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":0.1679188282558003,
           "proportion":0.8207520434237199
          },
         "1":{
           "omega":0.2120937673953722,
           "proportion":0.1693698006934513
          },
         "2":{
           "omega":13.84252711122189,
           "proportion":0.00987815588282877
          }
        },
       "Test":{
         "0":{
           "omega":0.08367159828032572,
           "proportion":0.9533274940567786
          },
         "1":{
           "omega":0.2493792697064242,
           "proportion":0.03716922067476962
          },
         "2":{
           "omega":34.20463703717275,
           "proportion":0.009503285268451747
          }
        }
      },
     "display order":2,
     "estimated parameters":37
    }
  },
 "input":{
   "file name":"/tmp/tmpfzf3u9m4/job_working_directory/000/2/working/./input.nex",
   "number of sequences":8,
   "number of sites":440,
   "partition count":1,
   "trees":{
     "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"
    }
  },
 "test results":{
   "LRT":3.465106677611402,
   "p-value":0.08841616008911996
  },
 "tested":{
   "0":{
     "B_FR_83_HXB2":"background",
     "B_US_83_RF":"background",
     "B_US_86_JRFL":"background",
     "B_US_90_WEAU160":"test",
     "D_CD_83_ELI":"background",
     "D_CD_83_NDK":"background",
     "D_CD_84_84ZR085":"background",
     "D_UG_94_94UG114":"background",
     "Node1":"background",
     "Node10":"background",
     "Node2":"background",
     "Node3":"background",
     "Node9":"background"
    }
  },
 "timers":{
   "Constrained BUSTED model fitting":{
     "order":3,
     "timer":14
    },
   "Overall":{
     "order":0,
     "timer":60
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":3
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":40
    }
  }
}