annotate test-data/CONTRASTFEL/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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   "headers":    [
["alpha", "Synonymous substitution rate at a site"],
    ["beta (background)", "Non-synonymous substitution rate at a site for background branches"],
    ["beta (Reference)", "Non-synonymous substitution rate at a site for Reference branches"],
    ["beta (Foreground)", "Non-synonymous substitution rate at a site for Foreground branches"],
    ["subs (Reference)", "Substitutions mapped to Reference branches"],
    ["subs (Foreground)", "Substitutions mapped to Foreground branches"],
    ["P-value (overall)", "P-value for the test that non-synonymous rates differ between any of the selected groups: Reference,Foreground"],
    ["Q-value (overall)", "Q-value for the test that non-synonymous rates differ between any of the selected groups: Reference,Foreground"],
    ["Permutation p-value", "Label permutation test for significant sites"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"]
    ]
  },
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond and Steven Weaver",
   "citation":"Mol Biol Evol (2021), (38)3 1184–1198",
   "contact":"[e-mail]",
   "help":"http://www.hyphy.org/methods/other/contrast-fel/",
   "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n    branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n    and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles. Version 0.6 adds detailed ancestral state reconstruction",
   "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported",
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       "site-filter":null,
       "site-save-filter":null
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   "version":"0.6"
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      [0.007227085618113572],
      [0.03135043533876745],
      [0.01483399068059511],
      [0.02479309690153406],
      [0.01019156779054619]
      ],
     "Log Likelihood":-732.8054883961942,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *Foreground*":        [
[0, 1]
        ],
       "non-synonymous/synonymous rate ratio for *Reference*":        [
[0.09151674358221767, 1]
        ],
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.1731767727713265, 1]
        ]
      },
     "display order":1,
     "estimated parameters":52
    },
   "Nucleotide GTR":{
     "AIC-c":1629.793347037039,
     "Equilibrium frequencies":      [
[0.3401587301587302],
      [0.1992063492063492],
      [0.2417460317460317],
      [0.2188888888888889]
      ],
     "Log Likelihood":-767.535828988769,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.04373838731205614,
       "Substitution rate from nucleotide C to nucleotide G":0.1358621201540092,
       "Substitution rate from nucleotide C to nucleotide T":2.440756055642126,
       "Substitution rate from nucleotide G to nucleotide T":0.05999797406604262
      },
     "display order":0,
     "estimated parameters":47
    }
  },
 "input":{
   "file name":"/Users/hverdonk/work/59/459e012d061afd4446c814f9634d17/pretend_DENV1_ref-noStopCodons.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
   "number of sequences":21,
   "number of sites":100,
   "partition count":1,
   "trees":{
     "0":"(PP564823_1_2023_10_06,((((((AY732475_1_1994,AY732480_1_1994,(((PP563832_1_2023_08_28,PP563826_1_2023_08_21,PP563831_1_2023_08_29)Node12,(PP563838_1_2023_09_30,PP563839_1_2023_09_29)Node17)Node11,PP563845_1_2023_10_22)Node10,(AY732482_1_2001,AB178040_1_2002)Node21)Node7,AY726553_1_2002)Node6,AY708047_1_2001)Node5,((AY732478_1_1991,AY726552_1_2002,AY732477_1_1991)Node29,AF298808_1_1998)Node28)Node4,(AB204803_1_2004,AB195673_1_2003)Node35)Node3,AF298807_1_1998)Node2,AY732474_1_1980)"
    }
  },
 "runtime":"2.5.81",
 "substitutions":{
    "0":{
      "0":{
        "root":"ATG"
        },
      "1":{
        "root":"AAC"
        },
      "10":{
        "root":"CCG"
        },
      "11":{
        "root":"TCT"
        },
      "12":{
        "root":"TTC"
        },
      "13":{
        "root":"AAT"
        },
      "14":{
        "root":"ATG"
        },
      "15":{
        "root":"CTG"
        },
      "16":{
        "root":"AAA"
        },
      "17":{
        "root":"CGC"
        },
      "18":{
        "root":"GCG"
        },
      "19":{
        "root":"AGA"
        },
      "2":{
        "root":"AAC"
        },
      "20":{
        "root":"AAC"
        },
      "21":{
        "root":"CGC"
        },
      "22":{
        "root":"GTG"
        },
      "23":{
        "root":"TCA"
        },
      "24":{
        "root":"ACT"
        },
      "25":{
        "PP564823_1_2023_10_06":"GGT",
        "root":"GTT"
        },
      "26":{
        "Node8":"TCA",
        "PP564823_1_2023_10_06":"TCA",
        "root":"CCA"
        },
      "27":{
        "root":"CAG"
        },
      "28":{
        "root":"TTG"
        },
      "29":{
        "root":"GCG"
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      "3":{
        "root":"CAA"
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      "30":{
        "root":"AAG"
        },
      "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"
        },
      "35":{
        "root":"GGA"
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      "36":{
        "root":"TTG"
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      "37":{
        "Node8":"CTT",
        "root":"CTC"
        },
      "38":{
        "root":"TCA"
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      "39":{
        "root":"GGC"
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      "4":{
        "PP563845_1_2023_10_22":"CGA",
        "root":"CGG"
        },
      "40":{
        "Node2":"CAG",
        "root":"CAA"
        },
      "41":{
        "root":"GGA"
        },
      "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",
        "root":"CTG"
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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":{
        "root":"CTA"
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      "54":{
        "root":"AGA"
        },
      "55":{
        "Node2":"TTC",
        "root":"TTT"
        },
      "56":{
        "root":"CTA"
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      "57":{
        "root":"GCC"
        },
      "58":{
        "root":"ATA"
        },
      "59":{
        "Node3":"CCT",
        "root":"CCC"
        },
      "6":{
        "root":"AAG"
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      "60":{
        "root":"CCA"
        },
      "61":{
        "root":"ACA"
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      "62":{
        "root":"GCA"
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      "63":{
        "Node2":"GGG",
        "root":"GGA"
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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"
        },
      "69":{
        "Node2":"GGT",
        "PP564823_1_2023_10_06":"AGC",
        "root":"GGC"
        },
      "7":{
        "root":"ACG"
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      "70":{
        "root":"TCA"
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      "71":{
        "root":"TTC"
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      "72":{
        "root":"AAG"
        },
      "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":{
        "root":"ATC"
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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"
        },
      "80":{
        "PP563838_1_2023_09_30":"CTG",
        "PP564823_1_2023_10_06":"TTA",
        "root":"CTA"
        },
      "81":{
        "root":"CGG"
        },
      "82":{
        "root":"GGT"
        },
      "83":{
        "PP563832_1_2023_08_28":"TTT",
        "root":"TTC"
        },
      "84":{
        "PP564823_1_2023_10_06":"AAA",
        "root":"AAG"
        },
      "85":{
        "root":"AAA"
        },
      "86":{
        "PP564823_1_2023_10_06":"GAG",
        "root":"GAA"
        },
      "87":{
        "root":"ATC"
        },
      "88":{
        "root":"TCA"
        },
      "89":{
        "root":"AGC"
        },
      "9":{
        "root":"CGA"
        },
      "90":{
        "root":"ATG"
        },
      "91":{
        "PP563845_1_2023_10_22":"TTG",
        "root":"CTG"
        },
      "92":{
        "PP564823_1_2023_10_06":"AAC",
        "root":"AAT"
        },
      "93":{
        "root":"ATA"
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      "94":{
        "root":"ATG"
        },
      "95":{
        "PP564823_1_2023_10_06":"AAC",
        "root":"AAT"
        },
      "96":{
        "PP564823_1_2023_10_06":"AGG",
        "root":"AGA"
        },
      "97":{
        "root":"AGG"
        },
      "98":{
        "root":"AAA"
        },
      "99":{
        "root":"AGA"
        }
      }
    },
 "tested":{
   "0":{
     "AB178040_1_2002":"background",
     "AB195673_1_2003":"background",
     "AB204803_1_2004":"background",
     "AF298807_1_1998":"background",
     "AF298808_1_1998":"background",
     "AY708047_1_2001":"background",
     "AY726552_1_2002":"background",
     "AY726553_1_2002":"background",
     "AY732474_1_1980":"background",
     "AY732475_1_1994":"background",
     "AY732477_1_1991":"background",
     "AY732478_1_1991":"background",
     "AY732480_1_1994":"background",
     "AY732482_1_2001":"background",
     "Node10":"Reference",
     "Node11":"Reference",
     "Node12":"Reference",
     "Node17":"Reference",
     "Node2":"background",
     "Node21":"background",
     "Node28":"background",
     "Node29":"Foreground",
     "Node3":"background",
     "Node35":"Reference",
     "Node4":"background",
     "Node5":"background",
     "Node6":"background",
     "Node7":"background",
     "PP563826_1_2023_08_21":"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":{
   "FEL analysis":{
     "order":2,
     "timer":4
    },
   "Model fitting":{
     "order":1,
     "timer":1
    },
   "Total time":{
     "order":0,
     "timer":5
    }
  }
}