Mercurial > repos > iuc > hyphy_bgm
view test-data/summary/nsp8.FEL.json @ 32:12c2453e5040 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
author | iuc |
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date | Sat, 27 Nov 2021 11:28:17 +0000 |
parents | 1c3a2f66373f |
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model"], ["LRT", "Likelihood ration 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":"spond@temple.edu", "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.\n ", "requirements":"in-frame codon alignment and a phylogenetic tree", "version":"2.1" }, "branch attributes":{ "0":{ "Node20":{ "Global MG94xREV":0.001634412620939209, "Nucleotide GTR":0.001684521619549293 }, "Node38":{ "Global MG94xREV":0.001735516186079463, "Nucleotide GTR":0.00168484920326581 }, "Node4":{ "Global MG94xREV":0.001634082124264937, "Nucleotide GTR":0.001683801387489096 }, "REFERENCE":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"REFERENCE" }, "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" }, "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ "Global MG94xREV":0.001732287231356377, "Nucleotide GTR":0.001682745450340891, "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" }, "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" }, "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ "Global MG94xREV":0.001731614563238503, "Nucleotide GTR":0.00168274558227101, "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" }, "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ "Global MG94xREV":0.001735723694712937, "Nucleotide GTR":0.001684401404203384, "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" }, "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ "Global MG94xREV":0.001732400229866267, "Nucleotide GTR":0.00168406792173386, "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" }, "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ "Global MG94xREV":0.001734572377168157, "Nucleotide GTR":0.001684975469042935, "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021" }, "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{ "Global MG94xREV":0.00173556721774995, "Nucleotide GTR":0.001684401583391051, "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021" }, "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{ "Global MG94xREV":0.001732287295543277, "Nucleotide GTR":0.001682745512695379, "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021" }, "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021" }, "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{ "Global MG94xREV":0.001733756934810247, "Nucleotide GTR":0.001684431017860219, "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" }, "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{ "Global MG94xREV":0.001733765377790725, "Nucleotide GTR":0.001684439221071522, "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021" }, "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021" }, "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{ "Global MG94xREV":0.001736016204276856, "Nucleotide GTR":0.00168443927661716, "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021" }, "epi_isl_1652105_hCoV_19_Singapore_561_2021":{ "Global MG94xREV":0.001733699177045456, "Nucleotide GTR":0.001685171120971631, "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021" }, "epi_isl_1652118_hCoV_19_Singapore_575_2021":{ "Global MG94xREV":0.001733317358386759, "Nucleotide GTR":0.001684401899924961, "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021" }, "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{ "Global MG94xREV":0.01050948252153795, "Nucleotide GTR":0.01020457779555702, "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human" }, "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.02683667587594947, "Nucleotide GTR":0.02592331511084145, "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human" }, "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.005257318397498607, "Nucleotide GTR":0.005093980037543817, "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human" }, "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.003479916225811642, "Nucleotide GTR":0.003379296026417724, "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_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":{ "Global MG94xREV":0.00346484907456443, "Nucleotide GTR":0.003372774424630234, "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human" }, "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.003473329356219227, "Nucleotide GTR":0.003374190595560375, "original name":"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_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.005214237519132295, "Nucleotide GTR":0.00505933790460295, "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human" }, "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":{ "Global MG94xREV":0.003464011570187254, "Nucleotide GTR":0.003373764235314068, "original name":"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" }, "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":{ "Global MG94xREV":0.005236219940276191, "Nucleotide GTR":0.005068409188375663, "original name":"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" }, "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.003464842731605314, "Nucleotide GTR":0.003372774424770855, "original 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"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":{ "Global MG94xREV":0.003472571057360136, "Nucleotide GTR":0.003376034743011948, "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" }, "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":{ "Global MG94xREV":0.003474988473611597, "Nucleotide GTR":0.003374190741831846, "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" }, "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{ "Global MG94xREV":0.003471294890480852, "Nucleotide GTR":0.003376937492543959, "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" } }, "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, 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":"fel.filter.default" } }, "fits":{ "Global MG94xREV":{ "AIC-c":2512.96200112621, "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":-1205.05897637469, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *background*": [ [0.4929148115423557, 1] ], "non-synonymous/synonymous rate ratio for *test*": [ [24.31954781803373, 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 } }, "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":{ 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