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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 15:09:44 +0000
parents a6619171428e
children
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34:a6619171428e 35:841557158611
1 {
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6 ],
7 "analysis":{
8 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
9 "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. v2.3 adds support for SRV",
10 "contact":"spond@temple.edu",
11 "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.",
12 "requirements":"in-frame codon alignment and a phylogenetic tree",
13 "version":"2.3"
14 },
15 "branch attributes":{
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22 "Full adaptive model (non-synonymous subs/site)":1e-10,
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24 "LRT":0,
25 "Nucleotide GTR":0.001685167654714891,
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28 ],
29 "Rate classes":1,
30 "Uncorrected P-value":1,
31 "original name":"Baboon",
32 "rate at which 2 nucleotides are changed instantly within a single codon":0
33 },
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36 "Baseline MG94xREV omega ratio":1.387276691142692,
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42 "Nucleotide GTR":0.2660536011315811,
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45 ],
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47 "Uncorrected P-value":0.2692231522977311,
48 "original name":"Cat",
49 "rate at which 2 nucleotides are changed instantly within a single codon":0.2039176940606485
50 },
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57 "Full adaptive model (synonymous subs/site)":1e-10,
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59 "Nucleotide GTR":0.001820258053351119,
60 "Rate Distributions": [
61 [10000000000, 1]
62 ],
63 "Rate classes":1,
64 "Uncorrected P-value":0.3081784202350423,
65 "original name":"Chimp",
66 "rate at which 2 nucleotides are changed instantly within a single codon":0
67 },
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82 "original name":"Cow",
83 "rate at which 2 nucleotides are changed instantly within a single codon":0.1380461206420348
84 },
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96 ],
97 "Rate classes":1,
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100 "rate at which 2 nucleotides are changed instantly within a single codon":0
101 },
102 "Human":{
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104 "Baseline MG94xREV omega ratio":1,
105 "Corrected P-value":1,
106 "Full adaptive model":0,
107 "Full adaptive model (non-synonymous subs/site)":1e-10,
108 "Full adaptive model (synonymous subs/site)":1e-10,
109 "LRT":0,
110 "Nucleotide GTR":0,
111 "Rate Distributions": [
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113 ],
114 "Rate classes":1,
115 "Uncorrected P-value":1,
116 "original name":"Human",
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135 },
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339 "data partitions":{
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344 "name":"absrel.filter.default"
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450 "display order":2,
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453 "Nucleotide GTR":{
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464 "Substitution rate from nucleotide A to nucleotide G":1,
465 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
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467 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
468 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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474 "input":{
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476 "number of sequences":10,
477 "number of sites":187,
478 "partition count":1,
479 "trees":{
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481 }
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487 "tested":16
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492 "Cat":"test",
493 "Chimp":"test",
494 "Cow":"test",
495 "Horse":"test",
496 "Human":"test",
497 "Mouse":"test",
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505 "Rat":"test",
506 "RhMonkey":"test"
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530 "Testing for selection":{
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533 }
534 }
535 }