annotate test-data/busted-out2-1.json @ 21:b3b775a4ae1f draft

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

{
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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":0,
 "branch attributes":{
   "0":{
     "B_FR_83_HXB2":{
       "MG94xREV with separate rates for branch sets":0.01243274064118979,
       "Nucleotide GTR":0.01178680392701259,
       "constrained":0.01256398347964253,
       "original name":"B_FR_83_HXB2",
       "unconstrained":0.01346367617740634
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     "B_US_83_RF":{
       "MG94xREV with separate rates for branch sets":0.02861520854418918,
       "Nucleotide GTR":0.02637179869727959,
       "constrained":0.02907713203932123,
       "original name":"B_US_83_RF",
       "unconstrained":0.03296423032791345
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     "B_US_86_JRFL":{
       "MG94xREV with separate rates for branch sets":0.01913497611653954,
       "Nucleotide GTR":0.01766254318226218,
       "constrained":0.01932498128977916,
       "original name":"B_US_86_JRFL",
       "unconstrained":0.02067264364489925
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     "B_US_90_WEAU160":{
       "MG94xREV with separate rates for branch sets":0.02258152057123029,
       "Nucleotide GTR":0.0208836028381146,
       "constrained":0.02318748492797678,
       "original name":"B_US_90_WEAU160",
       "unconstrained":0.02519768979779986
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     "D_CD_83_ELI":{
       "MG94xREV with separate rates for branch sets":0.02096470337130958,
       "Nucleotide GTR":0.01905599613120992,
       "constrained":0.02057807476219352,
       "original name":"D_CD_83_ELI",
       "unconstrained":0.02169258688744172
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     "D_CD_83_NDK":{
       "MG94xREV with separate rates for branch sets":0.01034012674036274,
       "Nucleotide GTR":0.009776698714183414,
       "constrained":0.0105101167818647,
       "original name":"D_CD_83_NDK",
       "unconstrained":0.01040169158313715
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     "D_CD_84_84ZR085":{
       "MG94xREV with separate rates for branch sets":0.03124894063248942,
       "Nucleotide GTR":0.02822254903672137,
       "constrained":0.03140845141419388,
       "original name":"D_CD_84_84ZR085",
       "unconstrained":0.03388014669054998
      },
     "D_UG_94_94UG114":{
       "MG94xREV with separate rates for branch sets":0.0597102708893009,
       "Nucleotide GTR":0.05323070232023583,
       "constrained":0.06218362660429492,
       "original name":"D_UG_94_94UG114",
       "unconstrained":0.06804948826756697
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     "Node1":{
       "MG94xREV with separate rates for branch sets":0.02639559777106507,
       "Nucleotide GTR":0.02355240508560319,
       "constrained":0.02779997592087442,
       "unconstrained":0.02940126303315396
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     "Node10":{
       "MG94xREV with separate rates for branch sets":0.00193736936681532,
       "Nucleotide GTR":0.002230248981703367,
       "constrained":0.001848018461605612,
       "unconstrained":0.001859856019153286
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     "Node2":{
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       "Nucleotide GTR":0.003949360371801276,
       "constrained":0.00346172246250584,
       "unconstrained":0.002261770932022259
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     "Node3":{
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       "constrained":0.01170820974676507,
       "unconstrained":0.01401270546560647
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       "Nucleotide GTR":0.004986123424162501,
       "constrained":0.005522033787153708,
       "unconstrained":0.005520113121560347
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   "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":      [
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      ],
     "name":"busted.filter.default"
    }
  },
 "fits":{
   "Constrained model":{
     "AIC-c":6398.612664722735,
     "Log Likelihood":-3168.021928691643,
     "Rate Distributions":{
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.6914129319908371
          },
         "1":{
           "omega":0,
           "proportion":0.07568144722655729
          },
         "2":{
           "omega":1,
           "proportion":0.2329056207826056
          }
        }
      },
     "display order":3,
     "estimated parameters":31
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6408.899382280021,
     "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":-3176.217093030587,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.231720664913378, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":28
    },
   "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":6391.938375474656,
     "Log Likelihood":-3163.666348620609,
     "Rate Distributions":{
       "Test":{
         "0":{
           "omega":0.1490485393860332,
           "proportion":0.02658974082564446
          },
         "1":{
           "omega":0.169565784922581,
           "proportion":0.9641001770967245
          },
         "2":{
           "omega":15.09387961636913,
           "proportion":0.009310082077631076
          }
        }
      },
     "display order":2,
     "estimated parameters":32
    }
  },
 "input":{
   "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/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":8.711160142067456,
   "p-value":0.006417496108925114
  },
 "tested":{
   "0":{
     "B_FR_83_HXB2":"test",
     "B_US_83_RF":"test",
     "B_US_86_JRFL":"test",
     "B_US_90_WEAU160":"test",
     "D_CD_83_ELI":"test",
     "D_CD_83_NDK":"test",
     "D_CD_84_84ZR085":"test",
     "D_UG_94_94UG114":"test",
     "Node1":"test",
     "Node10":"test",
     "Node2":"test",
     "Node3":"test",
     "Node9":"test"
    }
  },
 "timers":{
   "Constrained BUSTED model fitting":{
     "order":3,
     "timer":23
    },
   "Overall":{
     "order":0,
     "timer":133
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":4
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":105
    }
  }
}