Mercurial > repos > iuc > hyphy_strike_ambigs
view test-data/summary/nsp8.combined.fas.BGM.json @ 9:193dcaef2169 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
| author | iuc |
|---|---|
| date | Wed, 30 Mar 2022 00:21:15 +0000 |
| parents | 204ac950894d |
| children |
line wrap: on
line source
{ "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 } } }