Mercurial > repos > iuc > hyphy_bgm
diff test-data/summary/nsp8.BUSTED.json @ 27:1c3a2f66373f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:09:31 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.BUSTED.json Wed Jun 09 07:09:31 2021 +0000 @@ -0,0 +1,580 @@ +{ + "Evidence Ratios":{ + "constrained": [ +[0.9898739518379264, 0.991027168169301, 0.9898739518379268, 0.9897812891397899, 0.9906204835370439, 0.9853516617064797, 0.9880798288003553, 0.9889781190332573, 0.988350548699827, 0.989374526624819, 0.9897812891397899, 0.9927999621758878, 0.9898739523607402, 0.9898739518379268, 0.9853516617064797, 0.9898739518379268, 0.9930617996638492, 0.9898739518379268, 0.9956363652357774, 0.9953242584232271, 0.9898739518379268, 0.9927999621758878, 0.9906204835370439, 0.9909311149283309, 0.9898739518379268, 0.9888494594022271, 0.9898739518379268, 0.9942729604246417, 0.9875096976732132, 0.9910812249043462, 0.9889781181731668, 0.9953242584232271, 0.9888494594022271, 0.9888494594022271, 0.9883505486998261, 0.9965511193500521, 25.13531965114348, 0.9852148186803413, 0.9918415472526246, 0.9918415472526246, 0.9889781181731668, 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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" + }, + "background":1, + "branch attributes":{ + "0":{ + "Node20":{ + "MG94xREV with separate rates for branch sets":0.001634413111521572, + "Nucleotide GTR":0.001684521619549293, + "constrained":0.001693211721917988, + "unconstrained":0.001634737470752693 + }, + "Node38":{ + "MG94xREV with separate rates for branch sets":0.001735516181117074, + "Nucleotide GTR":0.00168484920326581, + "constrained":0.001746636597224389, + "unconstrained":0.001745922493640185 + }, + "Node4":{ + "MG94xREV with separate rates for branch sets":0.001634082124848593, + "Nucleotide GTR":0.001683801387489096, + "constrained":0.00169237478895786, + "unconstrained":0.001634679276807916 + }, + "REFERENCE":{ + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + 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"partition count":1, + "trees":{ + 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"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 + } + } +} \ No newline at end of file