Mercurial > repos > iuc > hyphy_summary
diff test-data/summary/nsp8.MEME.json @ 0:f304c108aa1f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:03:54 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.MEME.json Wed Jun 09 07:03:54 2021 +0000 @@ -0,0 +1,916 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [3.180864197338322, 2.543979863949704, 1, 4.771296296007484, 0, 0, 0.6666666666666666, 0, 0, -9.280586212023099, -9.280586212023099], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0.0002152055713864022, 5.380139284660055e-05, 1, 0.5537159057721711, 0, 0, 0.6666666666666666, 0, 0, -9.653547986238197, -9.653323462942367], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [3.192432742671397, 2.614421539287398, 1, 4.788649114007091, 0, 0, 0.6666666666666666, 0, 0, -9.282601941350496, -9.282601941350496], + [0, 0, 1, 1.464518485321612, 0, 0, 0.6666666666666666, 0, 0, -10.62393719963694, -10.62320682078165], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 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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 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"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 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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 + }, + 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+ } + } +} \ No newline at end of file