Mercurial > repos > iuc > hyphy_bgm
view test-data/summary/nsp8.RELAX.json @ 34:4515f2f64e13 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
| author | iuc |
|---|---|
| date | Thu, 18 Aug 2022 14:01:09 +0000 |
| parents | 1c3a2f66373f |
| children |
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[0.006455230577911434], [0.01122180073845716], [0.02433965804833868], [0.002295465694104339], [0.003990447484454917], [0.008655128485630147], [0.01755532734880559], [0.00629057695692368], [0.01093556617204019], [0.02371882618448924] ], "Log Likelihood":-1204.057620165384, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *Reference*": [ [0, 1] ], "non-synonymous/synonymous rate ratio for *Test*": [ [21.18256670135096, 1] ], "non-synonymous/synonymous rate ratio for *Unclassified*": [ [0.5156677179593993, 1] ] }, "display order":1, "estimated parameters":52 }, "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 }, "RELAX alternative":{ "AIC-c":2539.023758734034, "Log Likelihood":-1203.827668840701, "Rate Distributions":{ "Reference":{ "0":{ "omega":0, "proportion":0.3229316344832856 }, "1":{ "omega":0, "proportion":0.6561871399951409 }, "2":{ "omega":2.618905128891877, "proportion":0.02088122552157349 } }, "Synonymous site-to-site rates":{ "0":{ "proportion":0, "rate":0.8672539109745554 }, "1":{ "proportion":1, "rate":1 }, "2":{ "proportion":0, "rate":1.04385559910209 } }, "Test":{ "0":{ "omega":0, "proportion":0.3229316344832856 }, "1":{ "omega":0, "proportion":0.6561871399951409 }, "2":{ "omega":887.8019782663979, "proportion":0.02088122552157349 } } }, "display order":2, "estimated parameters":65 }, "RELAX null":{ "AIC-c":2540.205243445127, "Log Likelihood":-1205.43925064937, "Rate Distributions":{ "Reference":{ "0":{ "omega":0.01761845549263694, "proportion":0.1028887690453239 }, "1":{ "omega":0.1789488803563501, "proportion":0.8141260406522884 }, "2":{ "omega":5.480099329809248, "proportion":0.08298519030238755 } }, "Synonymous site-to-site rates":{ "0":{ "proportion":0, "rate":0.8690455710978635 }, "1":{ "proportion":1, "rate":1 }, "2":{ "proportion":0, "rate":1.043145103957073 } }, "Test":{ "0":{ "omega":0.01761845549263694, "proportion":0.1028887690453239 }, "1":{ "omega":0.1789488803563501, "proportion":0.8141260406522884 }, "2":{ "omega":5.480099329809248, "proportion":0.08298519030238755 } } }, "display order":3, "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":3.223163617336922, "p-value":0.07260318641568564, "relaxation or intensification parameter":7.051367447513434 }, "tested":{ "0":{ "Node20":"Test", "Node38":"Reference", "Node4":"Test", "REFERENCE":"Unclassified", "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"Unclassified", "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified", "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified", "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified", "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified", "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified", "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified", "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified", "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified", "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified", "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified", "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified", "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified", "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified", "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified", "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified", "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified", "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified", "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Unclassified", "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Unclassified", "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified", "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Unclassified", "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Unclassified", "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":"Unclassified", "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":"Unclassified", "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Unclassified", "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Unclassified", "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":"Unclassified", "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":"Unclassified", "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":"Unclassified", "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Unclassified" } }, "timers":{ "Overall":{ "order":0, "timer":67 }, "Preliminary model fitting":{ "order":1, "timer":5 }, "RELAX alternative model fitting":{ "order":3, "timer":50 }, "RELAX null model fitting":{ "order":4, "timer":12 } } }