annotate test-data/summary/nsp8.BUSTED.json @ 31:5fcd1ece3a6e 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"
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       "MG94xREV with separate rates for branch sets":0.003464842721698225,
       "Nucleotide GTR":0.003372774424770855,
       "constrained":0.003508044185651234,
       "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human",
       "unconstrained":0.003507815553802554
      },
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
       "MG94xREV with separate rates for branch sets":0.001735902729262228,
       "Nucleotide GTR":0.001686266012390882,
       "constrained":0.001736374314870017,
       "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human",
       "unconstrained":0.001735532172102446
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     "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
       "MG94xREV with separate rates for branch sets":0.003480097445970276,
       "Nucleotide GTR":0.003374436490976879,
       "constrained":0.003479100177235689,
       "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human",
       "unconstrained":0.003478891730919581
      },
     "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
       "MG94xREV with separate rates for branch sets":0.00347257104743095,
       "Nucleotide GTR":0.003376034743011948,
       "constrained":0.003518997887784842,
       "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human",
       "unconstrained":0.003517561264776653
      },
     "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
       "MG94xREV with separate rates for branch sets":0.003474988463675508,
       "Nucleotide GTR":0.003374190741831846,
       "constrained":0.003517174184123671,
       "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human",
       "unconstrained":0.00351929009659662
      },
     "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
       "MG94xREV with separate rates for branch sets":0.003471294880555319,
       "Nucleotide GTR":0.003376937492543959,
       "constrained":0.003517915599429177,
       "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human",
       "unconstrained":0.003516462270783854
      }
    },
   "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] 
      ],
     "name":"busted.filter.default"
    }
  },
 "fits":{
   "Constrained model":{
     "AIC-c":2537.370055580011,
     "Log Likelihood":-1205.042170647148,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":0.00623371489168318,
           "proportion":0.02824597255703105
          },
         "1":{
           "omega":0.1719986773053319,
           "proportion":0.8104926399157489
          },
         "2":{
           "omega":2.233103409549535,
           "proportion":0.16126138752722
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0,
           "rate":0.9507923294014373
          },
         "1":{
           "proportion":1,
           "rate":1
          },
         "2":{
           "proportion":0,
           "rate":1.059005087778388
          }
        },
       "Test":{
         "0":{
           "omega":0.9993683385761363,
           "proportion":2.155223602575912e-10
          },
         "1":{
           "omega":0.999707726011995,
           "proportion":2.155223602111413e-10
          },
         "2":{
           "omega":1,
           "proportion":0.9999999995689552
          }
        }
      },
     "display order":3,
     "estimated parameters":63
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":2512.962001126987,
     "Equilibrium frequencies":      [
[0.03825952761243274],
      [0.01370948533169502],
      [0.0238326285579188],
      [0.05169206288834598],
      [0.02910782227384961],
      [0.01043016700423795],
      [0.01813184740308045],
      [0.03932728586627101],
      [0.01035067712195123],
      [0.003708944282165923],
      [0.006447644771501305],
      [0.01398469573761802],
      [0.0283653688047424],
      [0.01016412464618009],
      [0.01766935821790241],
      [0.03832416445281453],
      [0.01521889661505549],
      [0.005453366858635389],
      [0.009480156518454269],
      [0.02056209812326697],
      [0.01157852606970437],
      [0.004148917752546374],
      [0.007212496554133422],
      [0.01564363009947405],
      [0.00411729822204095],
      [0.001475345962268018],
      [0.002564747797779777],
      [0.005562840210150803],
      [0.01128319250724396],
      [0.004043091272315801],
      [0.007028527343480687],
      [0.01524460789411934],
      [0.03592403244011121],
      [0.01287261047188149],
      [0.02237780168434643],
      [0.04853659885475865],
      [0.02733097915424774],
      [0.009793473186905268],
      [0.01702501611901085],
      [0.03692661100139533],
      [0.009718835644621534],
      [0.003482537371104292],
      [0.0060540580187001],
      [0.01313102107355921],
      [0.02663384763763138],
      [0.009543670983435077],
      [0.01659075888876379],
      [0.0359847236220365],
      [0.00848480075962617],
      [0.03199221880690793],
      [0.01801483181642438],
      [0.006455230577911434],
      [0.01122180073845716],
      [0.02433965804833868],
      [0.002295465694104339],
      [0.003990447484454917],
      [0.008655128485630147],
      [0.01755532734880559],
      [0.00629057695692368],
      [0.01093556617204019],
      [0.02371882618448924] 
      ],
     "Log Likelihood":-1205.058976375078,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.4929148114260853, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[24.31954749176878, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":51
    },
   "Nucleotide GTR":{
     "AIC-c":2633.0046471406,
     "Equilibrium frequencies":      [
[0.3251262626262627],
      [0.1799242424242424],
      [0.2026515151515151],
      [0.2922979797979798] 
      ],
     "Log Likelihood":-1247.247280799152,
     "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":0.3101631549852981,
       "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
       "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
       "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
      },
     "display order":0,
     "estimated parameters":69
    },
   "Unconstrained model":{
     "AIC-c":2538.426858070025,
     "Log Likelihood":-1204.550057961818,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":0,
           "proportion":0.02741862862724963
          },
         "1":{
           "omega":0.1719979491289183,
           "proportion":0.8111826871363725
          },
         "2":{
           "omega":2.232058479326601,
           "proportion":0.1613986842363778
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0,
           "rate":0.9502886367487763
          },
         "1":{
           "proportion":1,
           "rate":1
          },
         "2":{
           "proportion":0,
           "rate":1.059678592887729
          }
        },
       "Test":{
         "0":{
           "omega":0.9993684330797956,
           "proportion":0
          },
         "1":{
           "omega":0.999368433118802,
           "proportion":0
          },
         "2":{
           "omega":25.32658549655282,
           "proportion":1
          }
        }
      },
     "display order":2,
     "estimated parameters":64
    }
  },
 "input":{
   "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
   "number of sequences":32,
   "number of sites":198,
   "partition count":1,
   "trees":{
     "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
    }
  },
 "test results":{
   "LRT":0.9842253706597148,
   "p-value":0.3056667368082906
  },
 "tested":{
   "0":{
     "Node20":"test",
     "Node38":"background",
     "Node4":"test",
     "REFERENCE":"background",
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
     "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
     "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
     "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
     "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
     "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
     "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
     "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
     "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
     "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
     "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
     "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
    }
  },
 "timers":{
   "Constrained BUSTED model fitting":{
     "order":3,
     "timer":3
    },
   "Overall":{
     "order":0,
     "timer":76
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":6
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":66
    }
  }
}