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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 15:13:13 +0000 |
| parents | 1c3a2f66373f |
| children |
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negative/neutral evolution component"], ["p<sup>-</sup>", "Mixture distribution weight allocated to β<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"], ["β<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"], ["p<sup>+</sup>", "Mixture distribution weight allocated to β<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"], ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β<sup>+</sup> rate"], ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], ["MEME LogL", "Site Log-likelihood under the MEME model"], ["FEL LogL", "Site Log-likelihood under the FEL model"] ] }, "analysis":{ "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", "contact":"spond@temple.edu", "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", "requirements":"in-frame codon alignment and a phylogenetic tree", "version":"2.1.2" }, "branch attributes":{ "0":{ "Node20":{ "EBF site 101 (partition 1)":1, "EBF site 103 (partition 1)":1, "EBF site 116 (partition 1)":1, "EBF site 123 (partition 1)":1, "EBF site 125 (partition 1)":0.9999823899944797, "EBF site 126 (partition 1)":1, "EBF site 128 (partition 1)":1, "EBF site 133 (partition 1)":0.5654898147900533, "EBF site 134 (partition 1)":1, "EBF site 14 (partition 1)":1, "EBF site 140 (partition 1)":1, "EBF site 141 (partition 1)":1, "EBF site 145 (partition 1)":1, "EBF site 146 (partition 1)":1, "EBF site 148 (partition 1)":1, "EBF site 15 (partition 1)":1, "EBF site 156 (partition 1)":1, "EBF site 16 (partition 1)":1, "EBF site 160 (partition 1)":1, "EBF site 161 (partition 1)":1, "EBF site 163 (partition 1)":1, "EBF site 164 (partition 1)":1, "EBF site 170 (partition 1)":1, "EBF site 176 (partition 1)":1, "EBF site 179 (partition 1)":1, "EBF site 18 (partition 1)":1, "EBF site 187 (partition 1)":1, "EBF site 190 (partition 1)":1, "EBF site 198 (partition 1)":1, "EBF site 21 (partition 1)":1, "EBF site 23 (partition 1)":1, "EBF site 25 (partition 1)":1, "EBF site 27 (partition 1)":1, "EBF site 3 (partition 1)":1, "EBF site 30 (partition 1)":1, "EBF site 37 (partition 1)":1616.162948531769, "EBF site 39 (partition 1)":1, "EBF site 40 (partition 1)":1, "EBF site 5 (partition 1)":1, "EBF site 51 (partition 1)":0.9995339403671608, "EBF site 63 (partition 1)":1, "EBF site 67 (partition 1)":1, "EBF site 70 (partition 1)":1, "EBF site 73 (partition 1)":1, "EBF site 74 (partition 1)":1, "EBF site 76 (partition 1)":1, "EBF site 8 (partition 1)":1, "EBF site 81 (partition 1)":1, "EBF site 83 (partition 1)":1, "EBF site 85 (partition 1)":0.9998333727208876, "EBF site 88 (partition 1)":1, "EBF site 89 (partition 1)":1, "EBF site 9 (partition 1)":1, "EBF site 96 (partition 1)":0.9999780756681181, "EBF site 99 (partition 1)":1, "Global MG94xREV":0.001634413111541721, "Nucleotide GTR":0.001684521619549293 }, "Node38":{ "Global MG94xREV":0.001735516182878667, "Nucleotide GTR":0.00168484920326581 }, "Node4":{ "EBF site 101 (partition 1)":1, "EBF site 103 (partition 1)":1, "EBF site 116 (partition 1)":1, "EBF site 123 (partition 1)":1, "EBF site 125 (partition 1)":0.9999823935606595, "EBF site 126 (partition 1)":1, "EBF site 128 (partition 1)":1, "EBF site 133 (partition 1)":1e+26, "EBF site 134 (partition 1)":1, "EBF site 14 (partition 1)":1, "EBF site 140 (partition 1)":1, "EBF site 141 (partition 1)":1, "EBF site 145 (partition 1)":1, "EBF site 146 (partition 1)":1, "EBF site 148 (partition 1)":1, "EBF site 15 (partition 1)":1, "EBF site 156 (partition 1)":1, "EBF site 16 (partition 1)":1, "EBF site 160 (partition 1)":1, "EBF site 161 (partition 1)":1, "EBF site 163 (partition 1)":1, "EBF site 164 (partition 1)":1, "EBF site 170 (partition 1)":1, "EBF site 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1)":0.9999780801079843, "EBF site 99 (partition 1)":1, "Global MG94xREV":0.001634082124753167, "Nucleotide GTR":0.001683801387489096 }, "REFERENCE":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"REFERENCE" }, "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" }, "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ "Global MG94xREV":0.001732287228161539, "Nucleotide GTR":0.001682745450340891, "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" }, "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" }, "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ "Global MG94xREV":0.001731614560044905, "Nucleotide GTR":0.00168274558227101, "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" }, "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ "Global MG94xREV":0.001735723691511758, "Nucleotide GTR":0.001684401404203384, "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" }, "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ "Global MG94xREV":0.001732400226671219, "Nucleotide GTR":0.00168406792173386, "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" }, "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ "Global MG94xREV":0.001734572373969102, "Nucleotide GTR":0.001684975469042935, "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021" }, "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{ "Global MG94xREV":0.001735567214549057, "Nucleotide GTR":0.001684401583391051, "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021" }, "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{ "Global MG94xREV":0.001732287292348436, "Nucleotide GTR":0.001682745512695379, "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021" }, "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021" }, "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{ "Global MG94xREV":0.001733756931612698, "Nucleotide GTR":0.001684431017860219, "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" }, "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{ "Global MG94xREV":0.001733765374593157, "Nucleotide GTR":0.001684439221071522, "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021" }, "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021" }, "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{ "Global MG94xREV":0.001736016201075139, "Nucleotide GTR":0.00168443927661716, "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021" }, "epi_isl_1652105_hCoV_19_Singapore_561_2021":{ "Global MG94xREV":0.001733699173848011, "Nucleotide GTR":0.001685171120971631, "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021" }, "epi_isl_1652118_hCoV_19_Singapore_575_2021":{ "Global MG94xREV":0.001733317355190017, "Nucleotide GTR":0.001684401899924961, "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":{ "Global MG94xREV":0.01050948250215542, "Nucleotide GTR":0.01020457779555702, "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":{ "Global MG94xREV":0.02683667582570331, "Nucleotide GTR":0.02592331511084145, "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":{ "Global MG94xREV":0.005257318387802578, "Nucleotide GTR":0.005093980037543817, "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":{ "Global MG94xREV":0.003479916219393658, "Nucleotide GTR":0.003379296026417724, "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":{ "Global MG94xREV":0.003464849068174243, "Nucleotide GTR":0.003372774424630234, "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":{ "Global MG94xREV":0.003473329349813396, "Nucleotide GTR":0.003374190595560375, "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":{ "Global MG94xREV":0.00521423750951572, "Nucleotide GTR":0.00505933790460295, "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":{ "Global MG94xREV":0.003464011563798612, "Nucleotide GTR":0.003373764235314068, "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":{ "Global MG94xREV":0.005236219930619085, "Nucleotide GTR":0.005068409188375663, "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":{ "Global MG94xREV":0.003464842725215135, "Nucleotide GTR":0.003372774424770855, "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":{ "Global MG94xREV":0.001735902731024219, "Nucleotide GTR":0.001686266012390882, "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":{ "Global MG94xREV":0.00348009744950267, "Nucleotide GTR":0.003374436490976879, "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":{ "Global MG94xREV":0.003472571050955705, "Nucleotide GTR":0.003376034743011948, "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":{ "Global MG94xREV":0.003474988467202712, "Nucleotide GTR":0.003374190741831846, "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":{ "Global MG94xREV":0.003471294884078775, "Nucleotide GTR":0.003376937492543959, "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":{ "EBF site 101 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 103 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 116 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 123 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 125 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 126 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 128 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 133 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 134 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 14 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 140 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 141 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 145 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 146 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 148 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 15 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 156 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 16 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 160 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 161 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 163 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 164 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 170 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 176 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 179 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 18 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 187 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 190 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 198 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 21 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 23 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 25 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 27 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 3 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 30 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 37 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 39 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 40 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 5 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 51 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 63 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 67 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 70 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 73 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 74 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 76 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 8 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 81 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 83 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 85 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 88 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 89 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 9 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 96 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "EBF site 99 (partition 1)":{ "attribute type":"branch label", "display order":200 }, "Global MG94xREV":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "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":"meme.filter.default" } }, "fits":{ "Global MG94xREV":{ "AIC-c":2512.962001126494, "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], 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