view test-data/FEL/gene2.json @ 0:dd2d60b55e0d draft default tip

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

{
 "MLE":{
   "content":{
     "0":      [
[0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [9.722937713588191, 2.65346743038201e-07, 4.309348521470485, 2.099877387518221, 0.1473109512934778, 0.3766743601287894],
      [8.863430082988716, 2.887897339660802e-07, 4.819579247423198, 1.070265016280933, 0.300885592639103, 0.4212729418537841],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [1.057068606022313e-08, 3.296285981660705e-05, 2.171345179860732e-07, -1.732566890311205e-05, 1, 1.897943626902756e-08],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [4.867867373790146e-05, 6.527809284666965e-06, 6.885509176152527e-08, -4.181728872154622e-05, 1, 6.018530991786998e-09],
      [3.973171281416444e-06, 4.8792159251635, 2.816134959431011, 0.9723257537966461, 0.3241008268589686, 0.2461545703706566],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [4.164442444887993e-06, 3.862471585357244e-07, 1.309473750290936e-09, -8.728020160830852e-06, 1, 1.144593398604887e-10],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [7.885297421740413, 2.079286008090363e-07, 2.468390803602489, 2.000524429681379, 0.1572447941470875, 0.2157587212689601],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [12.39158212747011, 0.0001502635328722172, 5.763106077988476, 1.20857658631218, 0.2716142087143237, 0.5037453534948472],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [4.170058718806299e-06, 1.197623702229967e-05, 1.354520769494603e-09, -6.654469521194528e-06, 1, 1.183968392411284e-10],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [20.21550272153954, 1.660901513690031e-05, 3.064252525331256, 2.895583142426645, 0.08882262895826354, 0.2678421931996165],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [9.290913714941846, 0.0001037135369695749, 2.601107348573034, 2.02847757980642, 0.1543751806853721, 0.2273592960208547],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [7.609454923098985, 1.212606744231432e-06, 2.094845790572753, 2.205863512132154, 0.1374868873205098, 0.1831076539298388],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [8.818688908176565, 5.455512011916389e-05, 3.536603220006862, 1.625587915611213, 0.2023143895700279, 0.3091297323222607],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [6.094428690898675, 5.537673295529444e-06, 2.981128612467538, 1.270762232852181, 0.2596237343006303, 0.2605764437404245],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [6.036647663381378, 1.453748910915697e-05, 4.178594097883439, 1.269351043402544, 0.259888459075395, 0.3652452917688573],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [107.4663820022236, 5.216008707924475e-07, 2.659769287575728, 3.311487590436872, 0.068797188670217, 0.2324868572351921],
      [7.716139960537635, 3.121494021019207e-05, 4.283675209195019, 1.062450017507318, 0.3026570573017687, 0.3744302904218333],
      [0, 0, 0, 0, 1, 0],
      [8.904626254522967, 4.598479037951136e-08, 3.996375863616716, 1.40762938904556, 0.2354503271441786, 0.3493178409130618],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [4.093514277833543, 2.220034223104572e-10, 2.783281451084778, 0.9069889231385115, 0.3409146103568217, 0.2432828893792846],
      [5.247051127462107, 0.0001363123682242738, 3.35182703660018, 0.7997047903383496, 0.3711816470627252, 0.2929786945714314],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [5.247051127462107, 0.0001363123682242738, 3.35182703660018, 0.7997047903383496, 0.3711816470627252, 0.2929786945714314],
      [7.765241594927157, 2.072927156636369e-07, 4.085435842409801, 1.163027149382108, 0.2808386199341393, 0.3571024539138042],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0]
      ]
    },
   "headers":    [
["alpha", "Synonymous substitution rate at a site"],
    ["beta", "Non-synonymous substitution rate at a site"],
    ["alpha=beta", "The rate estimate under the neutral model"],
    ["LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"],
    ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
    ]
  },
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
   "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
   "contact":"[e-mail]",
   "info":"FEL (Fixed Effects Likelihood)\n    estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n    uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n    The estimates aggregate information over all branches,\n    so the signal is derived from\n    pervasive diversification or conservation. A subset of branches can be selected\n    for testing as well, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing.\n    Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis. Version 2.5 adds MH support.\n    ",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "settings":{
     "ci":0,
     "multihit":"None",
     "pvalue":0.1,
     "resample":0,
     "site-filter":{
       "site-filter":null,
       "site-save-filter":null
      },
     "srv":1
    },
   "version":"2.5"
  },
 "branch attributes":{
   "0":{
     "Node2":{
       "Global MG94xREV":0.01555447631320992,
       "Nucleotide GTR":0.01391650578382423
      },
     "Node3":{
       "Global MG94xREV":0.007028865074476463,
       "Nucleotide GTR":0.007313844682570613
      },
     "Node8":{
       "Global MG94xREV":0.006626243690924009,
       "Nucleotide GTR":0.006196659368038242
      },
     "PP563830_1_2023_09_02":{
       "Global MG94xREV":0,
       "Nucleotide GTR":1e-06,
       "original name":"PP563830_1_2023_09_02"
      },
     "PP563831_1_2023_08_29":{
       "Global MG94xREV":0.003308232804180055,
       "Nucleotide GTR":0.003339882520232537,
       "original name":"PP563831_1_2023_08_29"
      },
     "PP563832_1_2023_08_28":{
       "Global MG94xREV":0.003305901719100713,
       "Nucleotide GTR":0.003342518270787742,
       "original name":"PP563832_1_2023_08_28"
      },
     "PP563838_1_2023_09_30":{
       "Global MG94xREV":0.003316292450534825,
       "Nucleotide GTR":0.003339882520180704,
       "original name":"PP563838_1_2023_09_30"
      },
     "PP563839_1_2023_09_29":{
       "Global MG94xREV":0,
       "Nucleotide GTR":1e-06,
       "original name":"PP563839_1_2023_09_29"
      },
     "PP563845_1_2023_10_22":{
       "Global MG94xREV":0.005918187425081579,
       "Nucleotide GTR":0.007157676157708746,
       "original name":"PP563845_1_2023_10_22"
      },
     "PP564823_1_2023_10_06":{
       "Global MG94xREV":0.04453027608174031,
       "Nucleotide GTR":0.04195089101557686,
       "original name":"PP564823_1_2023_10_06"
      }
    },
   "attributes":{
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
  },
 "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]
      ],
     "name":"fel.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":1098.164180855893,
     "Equilibrium frequencies":      [
[0.04022787530103862],
      [0.01934493712337751],
      [0.03425741450905353],
      [0.01425856648080257],
      [0.03379960463533115],
      [0.01625368532572285],
      [0.0287832021345848],
      [0.01198009852897374],
      [0.03434841386947805],
      [0.01651759884459136],
      [0.02925055929127961],
      [0.01217462118004102],
      [0.04856425764989153],
      [0.02335376908798366],
      [0.04135654424169535],
      [0.01721335494628832],
      [0.01826098626758108],
      [0.008781414094422619],
      [0.01555076352482647],
      [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":-522.0389997890163,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.2130893675277186, 1]
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.05367140804417245, 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
    }
  },
 "input":{
   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/66/caf0861a1e46548e7f15d9b82a4920/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)"
    }
  },
 "runtime":"2.5.73",
 "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":{
   "FEL analysis":{
     "order":2,
     "timer":4
    },
   "Model fitting":{
     "order":1,
     "timer":1
    },
   "Total time":{
     "order":0,
     "timer":5
    }
  }
}