comparison test-data/absrel-out1.json @ 16:d6f4ff2aed07 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
author iuc
date Fri, 18 Sep 2020 21:08:45 +0000
parents 9da003917dcb
children
comparison
equal deleted inserted replaced
15:24742f335426 16:d6f4ff2aed07
1 { 1 {
2 "analysis":{ 2 "analysis":{
3 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
4 "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",
5 "contact":"spond@temple.edu",
3 "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.", 6 "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.",
4 "version":"2.0", 7 "requirements":"in-frame codon alignment and a phylogenetic tree",
5 "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", 8 "version":"2.2"
6 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", 9 },
7 "contact":"spond@temple.edu", 10 "branch attributes":{
8 "requirements":"in-frame codon alignment and a phylogenetic tree" 11 "0":{
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14 "Baseline MG94xREV omega ratio":0,
15 "Corrected P-value":1,
16 "Full adaptive model":0.001810407118394509,
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20 [0, 1]
21 ],
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23 "Uncorrected P-value":1,
24 "original name":"Baboon",
25 "rate at which 2 nucleotides are changed instantly within a single codon":0
26 },
27 "Cat":{
28 "Baseline MG94xREV":0.2286001363527903,
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30 "Corrected P-value":1,
31 "Full adaptive model":0.1219386838393392,
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37 ],
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41 "rate at which 2 nucleotides are changed instantly within a single codon":0
42 },
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52 ],
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55 "original name":"Chimp",
56 "rate at which 2 nucleotides are changed instantly within a single codon":0
57 },
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68 ],
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72 "rate at which 2 nucleotides are changed instantly within a single codon":0
73 },
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99 ],
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119 },
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133 },
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202 "rate at which 2 nucleotides are changed instantly within a single codon":0
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233 },
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246 "original name":"RhMonkey",
247 "rate at which 2 nucleotides are changed instantly within a single codon":0
248 }
249 },
250 "attributes":{
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252 "attribute type":"branch length",
253 "display order":1
254 },
255 "Baseline MG94xREV omega ratio":{
256 "attribute type":"branch label",
257 "display order":1
258 },
259 "Corrected P-value":{
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261 "display order":6
262 },
263 "Full adaptive model":{
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265 "display order":2
266 },
267 "LRT":{
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269 "display order":4
270 },
271 "Nucleotide GTR":{
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274 },
275 "Rate Distributions":{
276 "attribute type":"branch label",
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278 },
279 "Rate classes":{
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281 "display order":2
282 },
283 "Uncorrected P-value":{
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285 "display order":5
286 },
287 "original name":{
288 "attribute type":"node label",
289 "display order":-1
290 },
291 "rate at which 2 nucleotides are changed instantly within a single codon":{
292 "attribute type":"branch label",
293 "display order":7
294 }
295 }
296 },
297 "data partitions":{
298 "0":{
299 "coverage": [
300 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186]
301 ],
302 "name":"absrel.filter.default"
303 }
304 },
305 "fits":{
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375 "97.5%":12.07373117808175,
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386 "display order":1,
387 "estimated parameters":62
388 },
389 "Full adaptive model":{
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391 "Log Likelihood":-3415.824749853321,
392 "Rate Distributions":{
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394 "display order":2,
395 "estimated parameters":68
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397 "Nucleotide GTR":{
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408 "Substitution rate from nucleotide A to nucleotide G":1,
409 "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,
410 "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,
411 "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,
412 "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399
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414 "display order":0,
415 "estimated parameters":24
416 }
9 }, 417 },
10 "input":{ 418 "input":{
11 "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa", 419 "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
12 "number of sequences":10, 420 "number of sequences":10,
13 "number of sites":187, 421 "number of sites":187,
14 "partition count":1, 422 "partition count":1,
15 "trees":{ 423 "trees":{
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17 }
18 },
19 "fits":{
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32 "Substitution rate from nucleotide A to nucleotide G":1,
33 "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
34 "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
35 "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
36 "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
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107 "Rate Distributions":{
108 "Per-branch omega":{
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110 "Median":1.103169534345197,
111 "2.5%":0,
112 "97.5%":10000000000
113 }
114 },
115 "display order":1
116 },
117 "Full adaptive model":{
118 "Log Likelihood":-3414.992415597899,
119 "estimated parameters":60,
120 "AIC-c":6954.031265689993,
121 "Rate Distributions":{
122 },
123 "display order":2
124 }
125 },
126 "timers":{
127 "Overall":{
128 "timer":98,
129 "order":0
130 },
131 "Preliminary model fitting":{
132 "timer":0,
133 "order":1
134 },
135 "Baseline model fitting":{
136 "timer":1,
137 "order":2
138 },
139 "Complexity analysis":{
140 "timer":36,
141 "order":3
142 },
143 "Full adaptive model fitting":{
144 "timer":8,
145 "order":4
146 },
147 "Testing for selection":{
148 "timer":53,
149 "order":5
150 } 425 }
151 }, 426 },
152 "test results":{ 427 "test results":{
153 "P-value threshold":0.05, 428 "P-value threshold":0.05,
154 "tested":16, 429 "positive test results":0,
155 "positive test results":3 430 "tested":16
156 }, 431 },
157 "tested":{ 432 "tested":{
158 "0":{ 433 "0":{
434 "Baboon":"test",
435 "Cat":"test",
436 "Chimp":"test",
437 "Cow":"test",
438 "Horse":"test",
439 "Human":"test",
440 "Mouse":"test",
441 "Node1":"test",
442 "Node12":"test",
443 "Node2":"test",
444 "Node3":"test",
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456 } 478 }