Mercurial > repos > iuc > hyphy_annotate
diff test-data/summary/nsp8.RELAX.json @ 12:6efabd37807b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
| author | iuc |
|---|---|
| date | Tue, 07 Oct 2025 20:44:41 +0000 |
| parents | d088a1cca4a7 |
| children |
line wrap: on
line diff
--- a/test-data/summary/nsp8.RELAX.json Thu Mar 02 15:02:12 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,557 +0,0 @@ -{ - "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