Mercurial > repos > iuc > hyphy_summary
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
| author | iuc |
|---|---|
| date | Thu, 02 Mar 2023 15:14:24 +0000 |
| parents | f304c108aa1f |
| children |
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Biol Evol. 32(5):1365-71", "contact":"spond@temple.edu", "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). 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, "constrained":0, "original name":"REFERENCE", 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"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", "unconstrained":0.005289677385186297 }, "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":0.003464842721698225, "Nucleotide GTR":0.003372774424770855, "constrained":0.003508044185651234, "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", "unconstrained":0.003507815553802554 }, "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":0.001735902729262228, "Nucleotide GTR":0.001686266012390882, "constrained":0.001736374314870017, "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", "unconstrained":0.001735532172102446 }, "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":0.003480097445970276, "Nucleotide GTR":0.003374436490976879, "constrained":0.003479100177235689, "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", "unconstrained":0.003478891730919581 }, "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":0.00347257104743095, "Nucleotide GTR":0.003376034743011948, "constrained":0.003518997887784842, "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", "unconstrained":0.003517561264776653 }, "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":0.003474988463675508, "Nucleotide GTR":0.003374190741831846, "constrained":0.003517174184123671, "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", "unconstrained":0.00351929009659662 }, "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":0.003471294880555319, "Nucleotide GTR":0.003376937492543959, "constrained":0.003517915599429177, "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", "unconstrained":0.003516462270783854 } }, "attributes":{ "MG94xREV with separate rates for branch sets":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "constrained":{ "attribute type":"branch length", "display order":1 }, "original name":{ "attribute type":"node label", "display order":0 }, "unconstrained":{ "attribute type":"branch length", "display order":0 } } }, "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":"busted.filter.default" } }, "fits":{ "Constrained model":{ "AIC-c":2537.370055580011, "Log Likelihood":-1205.042170647148, "Rate Distributions":{ "Background":{ "0":{ "omega":0.00623371489168318, "proportion":0.02824597255703105 }, "1":{ "omega":0.1719986773053319, "proportion":0.8104926399157489 }, "2":{ "omega":2.233103409549535, "proportion":0.16126138752722 } }, "Synonymous site-to-site rates":{ "0":{ "proportion":0, "rate":0.9507923294014373 }, "1":{ "proportion":1, "rate":1 }, "2":{ "proportion":0, "rate":1.059005087778388 } }, "Test":{ "0":{ "omega":0.9993683385761363, "proportion":2.155223602575912e-10 }, "1":{ "omega":0.999707726011995, "proportion":2.155223602111413e-10 }, "2":{ "omega":1, "proportion":0.9999999995689552 } } }, "display order":3, "estimated parameters":63 }, "MG94xREV with separate rates for branch sets":{ "AIC-c":2512.962001126987, "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], 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Distributions":{ "non-synonymous/synonymous rate ratio for *background*": [ [0.4929148114260853, 1] ], "non-synonymous/synonymous rate ratio for *test*": [ [24.31954749176878, 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 }, "Unconstrained model":{ "AIC-c":2538.426858070025, "Log Likelihood":-1204.550057961818, "Rate Distributions":{ "Background":{ "0":{ "omega":0, "proportion":0.02741862862724963 }, "1":{ "omega":0.1719979491289183, "proportion":0.8111826871363725 }, "2":{ "omega":2.232058479326601, "proportion":0.1613986842363778 } }, "Synonymous site-to-site rates":{ "0":{ "proportion":0, "rate":0.9502886367487763 }, "1":{ "proportion":1, "rate":1 }, "2":{ "proportion":0, "rate":1.059678592887729 } }, "Test":{ "0":{ "omega":0.9993684330797956, "proportion":0 }, "1":{ "omega":0.999368433118802, "proportion":0 }, "2":{ "omega":25.32658549655282, "proportion":1 } } }, "display order":2, "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)" 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"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", 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"Unconstrained BUSTED model fitting":{ "order":2, "timer":66 } } }