Mercurial > repos > iuc > hyphy_strike_ambigs
comparison test-data/absrel-out2.json @ 11:31e7f5a25db3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author | iuc |
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date | Thu, 02 Mar 2023 15:15:02 +0000 |
parents | f5bbd4b34541 |
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10:f5bbd4b34541 | 11:31e7f5a25db3 |
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1 { | |
2 "Synonymous site-posteriors": [ | |
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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":{ | |
16 "0":{ | |
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19 "Baseline MG94xREV omega ratio":0, | |
20 "Corrected P-value":1, | |
21 "Full adaptive model":0.001888788495524889, | |
22 "Full adaptive model (non-synonymous subs/site)":1e-10, | |
23 "Full adaptive model (synonymous subs/site)":0.001888788495524889, | |
24 "LRT":0, | |
25 "Nucleotide GTR":0.001685167654714891, | |
26 "Rate Distributions": [ | |
27 [0, 1] | |
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 }, | |
34 "Cat":{ | |
35 "Baseline MG94xREV":0.2956038491638456, | |
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41 "LRT":0.8385257143854687, | |
42 "Nucleotide GTR":0.2660536011315811, | |
43 "Rate Distributions": [ | |
44 [1.406509052931997, 1] | |
45 ], | |
46 "Rate classes":1, | |
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 }, | |
51 "Chimp":{ | |
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53 "Baseline MG94xREV omega ratio":10000000000, | |
54 "Corrected P-value":1, | |
55 "Full adaptive model":0.001852710195778403, | |
56 "Full adaptive model (non-synonymous subs/site)":0.001852710195778403, | |
57 "Full adaptive model (synonymous subs/site)":1e-10, | |
58 "LRT":0.6095489899789754, | |
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 }, | |
68 "Cow":{ | |
69 "Baseline MG94xREV":0.2725380828787176, | |
70 "Baseline MG94xREV omega ratio":1.996288552263199, | |
71 "Corrected P-value":1, | |
72 "Full adaptive model":0.2767543531983568, | |
73 "Full adaptive model (non-synonymous subs/site)":0.2381665266426745, | |
74 "Full adaptive model (synonymous subs/site)":0.03858782655568219, | |
75 "LRT":3.11056227267909, | |
76 "Nucleotide GTR":0.2480198736772598, | |
77 "Rate Distributions": [ | |
78 [2.042233367641365, 1] | |
79 ], | |
80 "Rate classes":1, | |
81 "Uncorrected P-value":0.07889622593515888, | |
82 "original name":"Cow", | |
83 "rate at which 2 nucleotides are changed instantly within a single codon":0.1380461206420348 | |
84 }, | |
85 "Horse":{ | |
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87 "Baseline MG94xREV omega ratio":1.164040491954013, | |
88 "Corrected P-value":1, | |
89 "Full adaptive model":0.2320795562671627, | |
90 "Full adaptive model (non-synonymous subs/site)":0.1780556222700155, | |
91 "Full adaptive model (synonymous subs/site)":0.05402393399714727, | |
92 "LRT":0.2293786685804662, | |
93 "Nucleotide GTR":0.2090998951755368, | |
94 "Rate Distributions": [ | |
95 [1.174701177865617, 1] | |
96 ], | |
97 "Rate classes":1, | |
98 "Uncorrected P-value":0.393889915055757, | |
99 "original name":"Horse", | |
100 "rate at which 2 nucleotides are changed instantly within a single codon":0 | |
101 }, | |
102 "Human":{ | |
103 "Baseline MG94xREV":0, | |
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": [ | |
112 [1, 1] | |
113 ], | |
114 "Rate classes":1, | |
115 "Uncorrected P-value":1, | |
116 "original name":"Human", | |
117 "rate at which 2 nucleotides are changed instantly within a single codon":0.0009494209875164728 | |
118 }, | |
119 "Mouse":{ | |
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121 "Baseline MG94xREV omega ratio":0.5075430486034895, | |
122 "Corrected P-value":1, | |
123 "Full adaptive model":0.1314019024803463, | |
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126 "LRT":0, | |
127 "Nucleotide GTR":0.1181058300538561, | |
128 "Rate Distributions": [ | |
129 [0.5153237391744061, 1] | |
130 ], | |
131 "Rate classes":1, | |
132 "Uncorrected P-value":1, | |
133 "original name":"Mouse", | |
134 "rate at which 2 nucleotides are changed instantly within a single codon":0.02214869577417109 | |
135 }, | |
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149 "Uncorrected P-value":1, | |
150 "rate at which 2 nucleotides are changed instantly within a single codon":0.4322434210228028 | |
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214 "rate at which 2 nucleotides are changed instantly within a single codon":0.2354207827705045 | |
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228 "Rate classes":1, | |
229 "Uncorrected P-value":1, | |
230 "rate at which 2 nucleotides are changed instantly within a single codon":0 | |
231 }, | |
232 "Pig":{ | |
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234 "Baseline MG94xREV omega ratio":1.283370430439691, | |
235 "Corrected P-value":1, | |
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238 "Full adaptive model (synonymous subs/site)":0.04686450976579729, | |
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244 "Rate classes":1, | |
245 "Uncorrected P-value":0.3213796354214938, | |
246 "original name":"Pig", | |
247 "rate at which 2 nucleotides are changed instantly within a single codon":0 | |
248 }, | |
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252 "Corrected P-value":1, | |
253 "Full adaptive model":0.06783877994658692, | |
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263 "original name":"Rat", | |
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269 "Corrected P-value":1, | |
270 "Full adaptive model":0.003691831254195047, | |
271 "Full adaptive model (non-synonymous subs/site)":0.003691831254195047, | |
272 "Full adaptive model (synonymous subs/site)":1e-10, | |
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274 "Nucleotide GTR":0.003778804730491441, | |
275 "Rate Distributions": [ | |
276 [10000000000, 1] | |
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278 "Rate classes":1, | |
279 "Uncorrected P-value":0.2385766813428075, | |
280 "original name":"RhMonkey", | |
281 "rate at which 2 nucleotides are changed instantly within a single codon":0 | |
282 } | |
283 }, | |
284 "attributes":{ | |
285 "Baseline MG94xREV":{ | |
286 "attribute type":"branch length", | |
287 "display order":1 | |
288 }, | |
289 "Baseline MG94xREV omega ratio":{ | |
290 "attribute type":"branch label", | |
291 "display order":1 | |
292 }, | |
293 "Corrected P-value":{ | |
294 "attribute type":"branch label", | |
295 "display order":6 | |
296 }, | |
297 "Full adaptive model":{ | |
298 "attribute type":"branch length", | |
299 "display order":2 | |
300 }, | |
301 "Full adaptive model (non-synonymous subs/site)":{ | |
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304 }, | |
305 "Full adaptive model (synonymous subs/site)":{ | |
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308 }, | |
309 "LRT":{ | |
310 "attribute type":"branch label", | |
311 "display order":4 | |
312 }, | |
313 "Nucleotide GTR":{ | |
314 "attribute type":"branch length", | |
315 "display order":0 | |
316 }, | |
317 "Rate Distributions":{ | |
318 "attribute type":"branch label", | |
319 "display order":3 | |
320 }, | |
321 "Rate classes":{ | |
322 "attribute type":"branch label", | |
323 "display order":2 | |
324 }, | |
325 "Uncorrected P-value":{ | |
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327 "display order":5 | |
328 }, | |
329 "original name":{ | |
330 "attribute type":"node label", | |
331 "display order":-1 | |
332 }, | |
333 "rate at which 2 nucleotides are changed instantly within a single codon":{ | |
334 "attribute type":"branch label", | |
335 "display order":7 | |
336 } | |
337 } | |
338 }, | |
339 "data partitions":{ | |
340 "0":{ | |
341 "coverage": [ | |
342 [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] | |
343 ], | |
344 "name":"absrel.filter.default" | |
345 } | |
346 }, | |
347 "fits":{ | |
348 "Baseline MG94xREV":{ | |
349 "AIC-c":6938.369899478594, | |
350 "Equilibrium frequencies": [ | |
351 [0.04876086397632926], | |
352 [0.03982224127745371], | |
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412 ], | |
413 "Log Likelihood":-3399.656647852504, | |
414 "Rate Distributions":{ | |
415 "Per-branch delta":{ | |
416 "2.5%":0, | |
417 "97.5%":10.66318587577853, | |
418 "Mean":1.142287895998736, | |
419 "Median":0.2080459069952131 | |
420 }, | |
421 "Per-branch omega":{ | |
422 "2.5%":0, | |
423 "97.5%":2.028136557891868, | |
424 "Mean":666666667.5178814, | |
425 "Median":1 | |
426 }, | |
427 "Synonymous site-to-site rates":{ | |
428 "0":{ | |
429 "proportion":0.3499070593950995, | |
430 "rate":0.3584907731592092 | |
431 }, | |
432 "1":{ | |
433 "proportion":0.5579704535685105, | |
434 "rate":1.083607309819905 | |
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436 "2":{ | |
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438 "rate":2.93023662601063 | |
439 } | |
440 } | |
441 }, | |
442 "display order":1, | |
443 "estimated parameters":67 | |
444 }, | |
445 "Full adaptive model":{ | |
446 "AIC-c":6937.867430345418, | |
447 "Log Likelihood":-3399.405413285916, | |
448 "Rate Distributions":{ | |
449 }, | |
450 "display order":2, | |
451 "estimated parameters":67 | |
452 }, | |
453 "Nucleotide GTR":{ | |
454 "AIC-c":7112.857288723968, | |
455 "Equilibrium frequencies": [ | |
456 [0.3592490842490842], | |
457 [0.181959706959707], | |
458 [0.240018315018315], | |
459 [0.2187728937728937] | |
460 ], | |
461 "Log Likelihood":-3532.321213744258, | |
462 "Rate Distributions":{ | |
463 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087, | |
464 "Substitution rate from nucleotide A to nucleotide G":1, | |
465 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828, | |
466 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347, | |
467 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727, | |
468 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741 | |
469 }, | |
470 "display order":0, | |
471 "estimated parameters":24 | |
472 } | |
473 }, | |
474 "input":{ | |
475 "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta", | |
476 "number of sequences":10, | |
477 "number of sites":187, | |
478 "partition count":1, | |
479 "trees":{ | |
480 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)" | |
481 } | |
482 }, | |
483 "runtime":"2.5.36", | |
484 "test results":{ | |
485 "P-value threshold":0.05, | |
486 "positive test results":0, | |
487 "tested":16 | |
488 }, | |
489 "tested":{ | |
490 "0":{ | |
491 "Baboon":"test", | |
492 "Cat":"test", | |
493 "Chimp":"test", | |
494 "Cow":"test", | |
495 "Horse":"test", | |
496 "Human":"test", | |
497 "Mouse":"test", | |
498 "Node1":"test", | |
499 "Node12":"test", | |
500 "Node2":"test", | |
501 "Node3":"test", | |
502 "Node8":"test", | |
503 "Node9":"test", | |
504 "Pig":"test", | |
505 "Rat":"test", | |
506 "RhMonkey":"test" | |
507 } | |
508 }, | |
509 "timers":{ | |
510 "Baseline model fitting":{ | |
511 "order":2, | |
512 "timer":129 | |
513 }, | |
514 "Complexity analysis":{ | |
515 "order":3, | |
516 "timer":406 | |
517 }, | |
518 "Full adaptive model fitting":{ | |
519 "order":4, | |
520 "timer":46 | |
521 }, | |
522 "Overall":{ | |
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524 "timer":1006 | |
525 }, | |
526 "Preliminary model fitting":{ | |
527 "order":1, | |
528 "timer":0 | |
529 }, | |
530 "Testing for selection":{ | |
531 "order":5, | |
532 "timer":424 | |
533 } | |
534 } | |
535 } |