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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 15:17:27 +0000
parents d5d909979314
children
comparison
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33:d5d909979314 34:5fd8dc04d6af
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 },
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22 "Full adaptive model (non-synonymous subs/site)":1e-10,
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28 ],
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31 "original name":"Baboon",
32 "rate at which 2 nucleotides are changed instantly within a single codon":0
33 },
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50 },
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62 ],
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64 "Uncorrected P-value":0.3081784202350423,
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66 "rate at which 2 nucleotides are changed instantly within a single codon":0
67 },
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84 },
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96 ],
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101 },
102 "Human":{
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104 "Baseline MG94xREV omega ratio":1,
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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,
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113 ],
114 "Rate classes":1,
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116 "original name":"Human",
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344 "name":"absrel.filter.default"
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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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468 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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476 "number of sequences":10,
477 "number of sites":187,
478 "partition count":1,
479 "trees":{
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487 "tested":16
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492 "Cat":"test",
493 "Chimp":"test",
494 "Cow":"test",
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505 "Rat":"test",
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530 "Testing for selection":{
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534 }
535 }