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spond/aBSREL.json

Created September 19, 2021 02:19
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aBSREL.json
{
"analysis":{
"authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
"citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models",
"contact":"spond@temple.edu",
"info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.2"
},
"branch attributes":{
"0":{
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"Corrected P-value":1,
"Full adaptive model":0.5312805618928613,
"Full adaptive model (non-synonymous subs/site)":0.1775060658979208,
"Full adaptive model (synonymous subs/site)":0.3537744959949406,
"LRT":0,
"Nucleotide GTR":0.2520891951547508,
"Rate Distributions": [
[0, 0.7254035781677559],
[0.6336125698519234, 0.2745964218322441]
],
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"original name":"GA01G0585.1"
},
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"Full adaptive model (non-synonymous subs/site)":0.03793540646357412,
"Full adaptive model (synonymous subs/site)":0.07931077193129285,
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[0.009926255881601238, 0.7333295175862998],
[0.5946735596799082, 0.2666704824137002]
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"original name":"GA02G0672.1"
},
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"Full adaptive model (synonymous subs/site)":1.504537883893051,
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[0.2140013289306771, 0.6617946776468853]
],
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"original name":"GA02G0926.1"
},
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"original name":"GA03G2309.1"
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"original name":"GA09G1262.1"
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"original name":"GA10G0564.1"
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"Nucleotide GTR":0.09973069366117329,
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"original name":"GA10G2263.1"
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"Uncorrected P-value":0.5,
"original name":"GA10G2389.1"
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"LRT":0.7084435967262834,
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"original name":"GA11G1661.1"
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"GBAR_A11G023330_1":{
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"original name":"GBAR_A11G023330.1"
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"original name":"GBAR_D08G013260.1"
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"original name":"GBAR_D11G011330.1"
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"original name":"GBAR_D12G028160.1"
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"original name":"GHE13G27980"
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"GH_A07G113500_1":{
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"Full adaptive model (non-synonymous subs/site)":0.1135855673741071,
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"GH_D03G073900_1":{
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"name":"absrel.filter.default"
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"Rate Distributions":{
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"Substitution rate from nucleotide A to nucleotide G":1,
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"Substitution rate from nucleotide C to nucleotide T":1.002470252941546,
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"number of sequences":81,
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"NODE1613":"test",
"NODE1664":"test",
"NODE1665":"test",
"NODE1714":"test",
"NODE1740":"test",
"NODE180":"test",
"NODE19":"test",
"NODE20":"test",
"NODE228":"test",
"NODE255":"test",
"NODE258":"test",
"NODE259":"test",
"NODE307":"test",
"NODE330":"test",
"NODE352":"test",
"NODE353":"test",
"NODE354":"test",
"NODE358":"test",
"NODE380":"test",
"NODE429":"test",
"NODE46":"test",
"NODE47":"test",
"NODE472":"test",
"NODE473":"test",
"NODE499":"test",
"NODE501":"test",
"NODE525":"test",
"NODE527":"test",
"NODE530":"test",
"NODE531":"test",
"NODE628":"test",
"NODE654":"test",
"NODE709":"test",
"NODE710":"test",
"NODE73":"test",
"NODE736":"test",
"NODE74":"test",
"NODE742":"test",
"NODE743":"test",
"NODE75":"test",
"NODE76":"test",
"NODE77":"test",
"NODE788":"test",
"NODE789":"test",
"NODE835":"test",
"NODE876":"test",
"NODE877":"test",
"NODE878":"test",
"NODE879":"test",
"NODE880":"test",
"NODE931":"test",
"NODE957":"test",
"NODE958":"test"
}
},
"timers":{
"Baseline model fitting":{
"order":2,
"timer":264
},
"Complexity analysis":{
"order":3,
"timer":1563
},
"Full adaptive model fitting":{
"order":4,
"timer":1984
},
"Overall":{
"order":0,
"timer":83151
},
"Preliminary model fitting":{
"order":1,
"timer":13
},
"Testing for selection":{
"order":5,
"timer":79325
}
}
}
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