Mercurial > repos > iuc > hyphy_summary

comparison test-data/absrel-out2.json @ 6:81b23515db14 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:23:34 +0000
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5:11dd1a96ffe9 6:81b23515db14
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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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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62 ],
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84 },
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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,
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113 ],
114 "Rate classes":1,
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116 "original name":"Human",
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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 }