annotate test-data/BUSTED/gene2.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

{
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 "analysis":{
   "authors":"Sergei L Kosakovsky Pond",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439",
   "contact":"[e-mail]",
   "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. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n                               \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "settings":{
     "error-sink":1,
     "mss":"No",
     "multiple-hit":"None",
     "srv":"Yes"
    },
   "version":"4.6"
  },
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      [0.006472514015538997],
      [0.01534294594175388],
      [0.007378175514105413],
      [0.01306580710473399],
      [0.005438229413926055],
      [0.01559207164907205],
      [0.007497976053105356],
      [0.01327795856827995],
      [0.005526530758038588],
      [0.02204519218088164],
      [0.01060117775101382],
      [0.01877333269084459],
      [0.00781380661894053],
      [0.02001283201397348],
      [0.009623848489980729],
      [0.0170426073132688],
      [0.007093446860043523],
      [0.01681485300040535],
      [0.008085991904804354],
      [0.0143192595888557],
      [0.005959939409601683],
      [0.01708787828271292],
      [0.008217285364372072],
      [0.0145517635478013],
      [0.006056711836919557],
      [0.02416007116849923],
      [0.01161818898347029],
      [0.02057432977490965],
      [0.008563414755540757],
      [0.01095174735555056],
      [0.008072200842739543],
      [0.01913496685581441],
      [0.009201697278655068],
      [0.01629503140027161],
      [0.006782292004731834],
      [0.009351106613197152],
      [0.01655961626153459],
      [0.006892417094094173],
      [0.02749367841825353],
      [0.0132212670023302],
      [0.02341317633368553],
      [0.009744994946783913]
      ],
     "Log Likelihood":-522.0390000538857,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.2134874183278158, 1]
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.05375692390200871, 1]
        ]
      },
     "display order":1,
     "estimated parameters":26
    },
   "Nucleotide GTR":{
     "AIC-c":1130.795872905925,
     "Equilibrium frequencies":      [
[0.3347619047619048],
      [0.2033333333333333],
      [0.2466666666666667],
      [0.2152380952380952]
      ],
     "Log Likelihood":-546.2152441452704,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0,
       "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
       "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
       "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
      },
     "display order":0,
     "estimated parameters":19
    },
   "Unconstrained model":{
     "AIC-c":1135.480989915523,
     "Log Likelihood":-521.8563486162983,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":224.9667643065964,
           "proportion":0
          },
         "1":{
           "omega":0.1788885192362742,
           "proportion":0.5465744472573087
          },
         "2":{
           "omega":0.251168474136212,
           "proportion":0.4534255527426913
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         "3":{
           "omega":0.2024887349695371,
           "proportion":0
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.2729752444117259,
           "rate":0
          },
         "1":{
           "proportion":0,
           "rate":1.396781922073988e-08
          },
         "2":{
           "proportion":0.7270247555882741,
           "rate":1.375468981370307
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        },
       "Test":{
         "0":{
           "omega":223.2365630647954,
           "proportion":0
          },
         "1":{
           "omega":0.02758628794594435,
           "proportion":0.1008034141000489
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         "2":{
           "omega":0.05377704583904181,
           "proportion":0.8985911133771098
          },
         "3":{
           "omega":1,
           "proportion":0.0006054725228412919
          }
        }
      },
     "display order":2,
     "estimated parameters":43
    }
  },
 "input":{
   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/a4/7d2a9b33d4505019743b214dbd74ff/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
   "number of sequences":7,
   "number of sites":100,
   "partition count":1,
   "trees":{
     "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
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  },
 "runtime":"2.5.73",
 "substitutions":{
   "0":{
     "0":{
       "root":"ATG"
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     "1":{
       "root":"AAC"
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     "10":{
       "root":"CCG"
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     "11":{
       "root":"TCT"
      },
     "12":{
       "root":"TTC"
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     "13":{
       "root":"AAT"
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     "14":{
       "root":"ATG"
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     "15":{
       "root":"CTG"
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     "16":{
       "root":"AAA"
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     "17":{
       "root":"CGC"
      },
     "18":{
       "root":"GCG"
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     "19":{
       "root":"AGA"
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     "2":{
       "root":"AAC"
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     "20":{
       "root":"AAC"
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     "21":{
       "root":"CGC"
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     "22":{
       "root":"GTG"
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     "23":{
       "root":"TCA"
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     "24":{
       "root":"ACT"
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     "25":{
       "PP564823_1_2023_10_06":"GGT",
       "root":"GTT"
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     "26":{
       "Node8":"TCA",
       "PP564823_1_2023_10_06":"TCA",
       "root":"CCA"
      },
     "27":{
       "root":"CAG"
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     "28":{
       "root":"TTG"
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     "29":{
       "root":"GCG"
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     "3":{
       "root":"CAA"
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     "30":{
       "root":"AAG"
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     "31":{
       "root":"AGA"
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     "32":{
       "root":"TTC"
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     "33":{
       "root":"TCA"
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     "34":{
       "PP563831_1_2023_08_29":"GAA",
       "root":"AAA"
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     "35":{
       "root":"GGA"
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     "36":{
       "root":"TTG"
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     "37":{
       "Node8":"CTT",
       "root":"CTC"
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     "38":{
       "root":"TCA"
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     "39":{
       "root":"GGC"
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     "4":{
       "PP563845_1_2023_10_22":"CGA",
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     "40":{
       "Node2":"CAG",
       "root":"CAA"
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     "41":{
       "root":"GGA"
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     "42":{
       "root":"CCC"
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     "43":{
       "root":"ATG"
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     "44":{
       "root":"AAA"
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     "45":{
       "PP564823_1_2023_10_06":"ATG",
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     "46":{
       "root":"GTG"
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     "47":{
       "root":"ATG"
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     "48":{
       "root":"GCT"
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     "49":{
       "Node3":"TTT",
       "root":"TTC"
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     "5":{
       "PP564823_1_2023_10_06":"AAG",
       "root":"AAA"
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     "50":{
       "root":"ATA"
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     "51":{
       "root":"GCA"
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     "52":{
       "root":"TTC"
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     "53":{
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     "54":{
       "root":"AGA"
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     "55":{
       "Node2":"TTC",
       "root":"TTT"
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     "56":{
       "root":"CTA"
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     "57":{
       "root":"GCC"
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     "58":{
       "root":"ATA"
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     "59":{
       "Node3":"CCT",
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     "6":{
       "root":"AAG"
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     "60":{
       "root":"CCA"
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     "61":{
       "root":"ACA"
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     "62":{
       "root":"GCA"
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     "63":{
       "Node2":"GGG",
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     "64":{
       "root":"ATT"
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     "65":{
       "root":"TTG"
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     "66":{
       "root":"GCT"
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     "67":{
       "root":"AGA"
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     "68":{
       "root":"TGG"
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     "69":{
       "Node2":"GGT",
       "PP564823_1_2023_10_06":"AGC",
       "root":"GGC"
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     "7":{
       "root":"ACG"
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     "70":{
       "root":"TCA"
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     "71":{
       "root":"TTC"
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     "72":{
       "root":"AAG"
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     "73":{
       "root":"AAG"
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     "74":{
       "root":"AAT"
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     "75":{
       "root":"GGA"
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     "76":{
       "root":"GCG"
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     "77":{
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     "78":{
       "root":"AAA"
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     "79":{
       "root":"GTG"
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     "8":{
       "PP564823_1_2023_10_06":"GGT",
       "root":"GCT"
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     "80":{
       "PP563838_1_2023_09_30":"CTG",
       "PP564823_1_2023_10_06":"TTA",
       "root":"CTA"
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     "81":{
       "root":"CGG"
      },
     "82":{
       "root":"GGT"
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     "83":{
       "PP563832_1_2023_08_28":"TTT",
       "root":"TTC"
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     "84":{
       "PP564823_1_2023_10_06":"AAA",
       "root":"AAG"
      },
     "85":{
       "root":"AAA"
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     "86":{
       "PP564823_1_2023_10_06":"GAG",
       "root":"GAA"
      },
     "87":{
       "root":"ATC"
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     "88":{
       "root":"TCA"
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     "89":{
       "root":"AGC"
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     "9":{
       "root":"CGA"
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     "90":{
       "root":"ATG"
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     "91":{
       "PP563845_1_2023_10_22":"TTG",
       "root":"CTG"
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     "92":{
       "PP564823_1_2023_10_06":"AAC",
       "root":"AAT"
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     "93":{
       "root":"ATA"
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     "94":{
       "root":"ATG"
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     "95":{
       "PP564823_1_2023_10_06":"AAC",
       "root":"AAT"
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     "96":{
       "PP564823_1_2023_10_06":"AGG",
       "root":"AGA"
      },
     "97":{
       "root":"AGG"
      },
     "98":{
       "root":"AAA"
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     "99":{
       "root":"AGA"
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    }
  },
 "test results":{
   "LRT":0,
   "p-value":0.5
  },
 "tested":{
   "0":{
     "Node2":"test",
     "Node3":"test",
     "Node8":"test",
     "PP563830_1_2023_09_02":"background",
     "PP563831_1_2023_08_29":"background",
     "PP563832_1_2023_08_28":"background",
     "PP563838_1_2023_09_30":"background",
     "PP563839_1_2023_09_29":"background",
     "PP563845_1_2023_10_22":"background",
     "PP564823_1_2023_10_06":"background"
    }
  },
 "timers":{
   "Overall":{
     "order":0,
     "timer":30
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":2
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":26
    }
  }
}