Mercurial > repos > iuc > hyphy_fubar
diff test-data/summary/nsp8.RELAX.json @ 27:8741542f9bc8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:07:10 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.RELAX.json Wed Jun 09 07:07:10 2021 +0000 @@ -0,0 +1,557 @@ +{ + "Synonymous site-posteriors": [ +[1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1], + [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] + ], + "analysis":0, + "branch attributes":{ + "0":{ + "Node20":{ + "MG94xREV with separate rates for branch sets":0.001634892352012191, + "Nucleotide GTR":0.001684521619549293, + "RELAX alternative":0.001888715982590274, + "RELAX null":0.001729201145341893 + }, + "Node38":{ + "MG94xREV with separate rates for branch sets":0.001919664136946674, + "Nucleotide GTR":0.00168484920326581, + "RELAX alternative":0.001886373803275281, + "RELAX null":0.001757668602191916 + }, + "Node4":{ + "MG94xREV with separate rates for branch sets":0.001634608725455373, + "Nucleotide GTR":0.001683801387489096, + "RELAX alternative":0.001736927843216757, + "RELAX null":0.001719649158870973 + }, + "REFERENCE":{ + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + "RELAX alternative":0, + "RELAX null":0, + "original name":"REFERENCE" + }, + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + "RELAX alternative":0, + "RELAX null":0, + "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" + }, + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ + "MG94xREV with separate rates for branch sets":0.001728428276944542, + "Nucleotide GTR":0.001682745450340891, + "RELAX alternative":0.001737560358174388, + "RELAX null":0.001737701430364698, + "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" + }, + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + "RELAX alternative":0, + "RELAX null":0, + "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" + }, + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ + "MG94xREV with separate rates for branch sets":0.001727412678204142, + "Nucleotide GTR":0.00168274558227101, + "RELAX alternative":0.001722861223551411, + "RELAX null":0.001721507731204673, + "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" + }, + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ + "MG94xREV with separate rates for branch sets":0.001731169182640301, + "Nucleotide GTR":0.001684401404203384, + "RELAX alternative":0.00172720734036594, + "RELAX null":0.001726404293760867, + "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" + }, + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ + "MG94xREV with separate rates for branch sets":0.00172839429492474, + "Nucleotide GTR":0.00168406792173386, + "RELAX alternative":0.001738200894069104, + "RELAX null":0.001737804594988544, + "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" + }, + "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ + "MG94xREV with separate rates for branch sets":0.001731480328068411, + "Nucleotide GTR":0.001684975469042935, + "RELAX alternative":0.00173051284681069, + "RELAX null":0.00172967207566356, + "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021" + }, + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{ + "MG94xREV with separate rates for branch sets":0.001732570341711745, + "Nucleotide GTR":0.001684401583391051, + "RELAX alternative":0.001742601253810536, + "RELAX null":0.001742131810362083, + "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021" + }, + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{ + "MG94xREV with separate rates for branch sets":0.001728428524856767, + "Nucleotide GTR":0.001682745512695379, + "RELAX alternative":0.001737560077236944, + "RELAX null":0.001737700138099048, + "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021" + }, + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{ + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + "RELAX alternative":0, + "RELAX null":0, + "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021" + }, + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{ + "MG94xREV with separate rates for branch sets":0.001730278960152961, + "Nucleotide GTR":0.001684431017860219, + "RELAX alternative":0.001731585452394539, + "RELAX null":0.001730940698634506, + "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" + }, + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{ + "MG94xREV with separate rates for branch sets":0.001730283048611941, + "Nucleotide GTR":0.001684439221071522, + "RELAX alternative":0.001731571223917744, + "RELAX null":0.001730939668085807, + "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021" + }, + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{ + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + "RELAX alternative":0, + "RELAX null":0, + "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021" + }, + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{ + "MG94xREV with separate rates for branch sets":0.001732590464662458, + "Nucleotide GTR":0.00168443927661716, + "RELAX alternative":0.001742601811734028, + "RELAX null":0.00174213227832234, + "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021" + }, + "epi_isl_1652105_hCoV_19_Singapore_561_2021":{ + "MG94xREV with separate rates for branch sets":0.001730912430514071, + "Nucleotide GTR":0.001685171120971631, + "RELAX alternative":0.001729942855612116, + "RELAX null":0.001729323731291246, + "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021" + }, + "epi_isl_1652118_hCoV_19_Singapore_575_2021":{ + "MG94xREV with separate rates for branch sets":0.00173012682067509, + "Nucleotide GTR":0.001684401899924961, + "RELAX alternative":0.001728421813161176, + "RELAX null":0.001727458069395059, + "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":{ + "MG94xREV with separate rates for branch sets":0.01048097601700974, + "Nucleotide GTR":0.01020457779555702, + "RELAX alternative":0.01047086585093888, + "RELAX null":0.01046479928106623, + "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":{ + "MG94xREV with separate rates for branch sets":0.02680857528731593, + "Nucleotide GTR":0.02592331511084145, + "RELAX alternative":0.02703815482394115, + "RELAX null":0.02704254951161574, + "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":{ + "MG94xREV with separate rates for branch sets":0.005248107101099727, + "Nucleotide GTR":0.005093980037543817, + "RELAX alternative":0.005295485335504809, + "RELAX null":0.005297040611322862, + "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":{ + "MG94xREV with separate rates for branch sets":0.003471698011425016, + "Nucleotide GTR":0.003379296026417724, + "RELAX alternative":0.003464800281543841, + "RELAX null":0.003462025084915378, + "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":{ + "MG94xREV with separate rates for branch sets":0.003457568744877869, + "Nucleotide GTR":0.003372774424630234, + "RELAX alternative":0.003496418535007078, + "RELAX null":0.003498104759780586, + "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":{ + "MG94xREV with separate rates for branch sets":0.003467133888186825, + "Nucleotide GTR":0.003374190595560375, + "RELAX alternative":0.003457734642580653, + "RELAX null":0.00345485979388556, + "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":{ + "MG94xREV with separate rates for branch sets":0.005201716536487767, + "Nucleotide GTR":0.00505933790460295, + "RELAX alternative":0.005204536236229277, + "RELAX null":0.005202316870638489, + "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":{ + "MG94xREV with separate rates for branch sets":0.003459439638886199, + "Nucleotide GTR":0.003373764235314068, + "RELAX alternative":0.003478792275254122, + "RELAX null":0.003479579349366638, + "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":{ + "MG94xREV with separate rates for branch sets":0.005223283065443013, + "Nucleotide GTR":0.005068409188375663, + "RELAX alternative":0.005275186961139124, + "RELAX null":0.005276641027676963, + "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":{ + "MG94xREV with separate rates for branch sets":0.003458770057493741, + "Nucleotide GTR":0.003372774424770855, + "RELAX alternative":0.00349755862857714, + "RELAX null":0.003499034126859038, + "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_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":{ + "MG94xREV with separate rates for branch sets":0.001732985715005558, + "Nucleotide GTR":0.001686266012390882, + "RELAX alternative":0.001733951893303371, + "RELAX null":0.001733155339598253, + "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_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":{ + "MG94xREV with separate rates for branch sets":0.003473875391185204, + "Nucleotide GTR":0.003374436490976879, + "RELAX alternative":0.003475120495681648, + "RELAX null":0.003473518149074519, + "original name":"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_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{ + "MG94xREV with separate rates for branch sets":0.003465962437529985, + "Nucleotide GTR":0.003376034743011948, + "RELAX alternative":0.003505853316276177, + "RELAX null":0.00350745511719164, + "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":{ + "MG94xREV with separate rates for branch sets":0.003468563552578822, + "Nucleotide GTR":0.003374190741831846, + "RELAX alternative":0.003507645115982479, + "RELAX null":0.003508905377887805, + "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":{ + "MG94xREV with separate rates for branch sets":0.003465082951850039, + "Nucleotide GTR":0.003376937492543959, + "RELAX alternative":0.003504702597413055, + "RELAX null":0.003506633016642548, + "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":{ + "MG94xREV with separate rates for branch sets":{ + "attribute type":"branch length", + "display order":1 + }, + "Nucleotide GTR":{ + "attribute type":"branch length", + "display order":0 + }, + "RELAX alternative":{ + "attribute type":"branch length", + "display order":2 + }, + "RELAX null":{ + "attribute type":"branch length", + "display order":3 + }, + "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":"relax.filter.default" + } + }, + "fits":{ + "MG94xREV with separate rates for branch sets":{ + "AIC-c":2512.992528250552, + "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":-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 + } + } +} \ No newline at end of file