Mercurial > repos > iuc > hyphy_fade

{
 "analysis":{
   "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",
   "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",
   "contact":"apoon42@uwo.ca",
   "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data.  Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"1.2"
  },
 "branch attributes":{
   "0":{
     "Node10":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node12":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node13":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node16":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node19":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node2":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node20":{
       "models.codon.MG_REV.ModelDescription":0.001732564301319626
      },
     "Node23":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node24":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node27":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node28":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node29":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node3":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node30":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node33":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node34":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node35":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node36":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node38":{
       "models.codon.MG_REV.ModelDescription":0.001730721769143463
      },
     "Node4":{
       "models.codon.MG_REV.ModelDescription":0.001731994998894883
      },
     "Node40":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node43":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node44":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node47":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node50":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node54":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node57":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node58":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node8":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "REFERENCE":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
       "models.codon.MG_REV.ModelDescription":0.001729346788706704
      },
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
       "models.codon.MG_REV.ModelDescription":0.001726770081665013
      },
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
       "models.codon.MG_REV.ModelDescription":0.001730890984495782
      },
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
       "models.codon.MG_REV.ModelDescription":0.001729521179312332
      },
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
       "models.codon.MG_REV.ModelDescription":0.00173187799003057
      },
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
       "models.codon.MG_REV.ModelDescription":0.001731880362018201
      },
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
       "models.codon.MG_REV.ModelDescription":0.001729347411994937
      },
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
       "models.codon.MG_REV.ModelDescription":0.001731050783674516
      },
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
       "models.codon.MG_REV.ModelDescription":0.001731182381236102
      },
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
       "models.codon.MG_REV.ModelDescription":0.001732532467960361
      },
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
       "models.codon.MG_REV.ModelDescription":0.001730310938171899
      },
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
       "models.codon.MG_REV.ModelDescription":0.001730892114618073
      },
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.010477277172687
      },
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.0267904473393482
      },
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.005246785993713827
      },
     "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.003470769604618349
      },
     "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.003457492024366724
      },
     "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.003467086067652968
      },
     "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.005199945527312524
      },
     "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":{
       "models.codon.MG_REV.ModelDescription":0.003459351766803247
      },
     "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":{
       "models.codon.MG_REV.ModelDescription":0.0052232197685525
      },
     "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.003458730279363404
      },
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.001734049878603634
      },
     "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":{
       "models.codon.MG_REV.ModelDescription":0.003472162792845677
      },
     "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":{
       "models.codon.MG_REV.ModelDescription":0.003466781435751312
      },
     "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":{
       "models.codon.MG_REV.ModelDescription":0.003467395894648151
      },
     "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
       "models.codon.MG_REV.ModelDescription":0.003463960996259906
      }
    },
   "attributes":{
     "models.codon.MG_REV.ModelDescription":{
       "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":"bgm.filter.default"
    }
  },
 "fits":{
   "models.codon.MG_REV.ModelDescription":{
     "AIC-c":2565.76651309329,
     "Log Likelihood":-1205.948282908683,
     "Rate Distributions":null,
     "display order":0,
     "estimated parameters":76
    }
  },
 "input":{
   "datatype":"codon",
   "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
   "number of sequences":32,
   "number of sites":198,
   "trees":{
     "0":"((((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)Node3,(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)Node13,(epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)Node16)Node12)Node10)Node8)Node2,((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)Node24,((((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)Node30,((((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)Node40)Node38)Node36,((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)Node44,(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)Node47)Node43)Node35,(epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021)Node50)Node34,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021)Node33)Node29,(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)Node54)Node28,((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)Node58,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021)Node57)Node27)Node23)Node19,REFERENCE)"
    }
  },
 "settings":{
   "burn-in":10000,
   "data-type":"codon",
   "max-parents":1,
   "min-subs":1,
   "samples":100,
   "steps":100000,
   "threshold":0.5
  },
 "tested":0,
 "timers":{
   "Baseline fit":{
     "order":1,
     "timer":4
    },
   "Network inference":{
     "order":2,
     "timer":0
    },
   "Overall":{
     "order":0,
     "timer":4
    }
  }
}
author	iuc
date	Thu, 18 Aug 2022 14:04:52 +0000
parents	60eec78ee26f
children