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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 15:10:19 +0000
parents 7207313de5a8
children
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33:7207313de5a8 34:5eb9d7217640
1 {
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",
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.",
7 "requirements":"in-frame codon alignment and a phylogenetic tree",
8 "version":"2.2"
9 },
10 "branch attributes":{
11 "0":{
12 "Baboon":{
13 "Baseline MG94xREV":0.001816807585564731,
14 "Baseline MG94xREV omega ratio":0,
15 "Corrected P-value":1,
16 "Full adaptive model":0.001810407118394509,
17 "LRT":0,
18 "Nucleotide GTR":0.001678881906620672,
19 "Rate Distributions": [
20 [0, 1]
21 ],
22 "Rate classes":1,
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,
29 "Baseline MG94xREV omega ratio":1.403298474422089,
30 "Corrected P-value":1,
31 "Full adaptive model":0.1219386838393392,
32 "LRT":1.644967676056694,
33 "Nucleotide GTR":0.265904547400163,
34 "Rate Distributions": [
35 [0.2130519766306851, 0.6352283641519592],
36 [2.628217450705319, 0.3647716358480408]
37 ],
38 "Rate classes":2,
39 "Uncorrected P-value":0.171730764045231,
40 "original name":"Cat",
41 "rate at which 2 nucleotides are changed instantly within a single codon":0
42 },
43 "Chimp":{
44 "Baseline MG94xREV":0.001840311209746262,
45 "Baseline MG94xREV omega ratio":10000000000,
46 "Corrected P-value":1,
47 "Full adaptive model":0.001841979303044237,
48 "LRT":0.6159123786974305,
49 "Nucleotide GTR":0.001816713800925801,
50 "Rate Distributions": [
51 [10000000000, 1]
52 ],
53 "Rate classes":1,
54 "Uncorrected P-value":0.3069983227523322,
55 "original name":"Chimp",
56 "rate at which 2 nucleotides are changed instantly within a single codon":0
57 },
58 "Cow":{
59 "Baseline MG94xREV":0.2070244948790512,
60 "Baseline MG94xREV omega ratio":2.153434974462683,
61 "Corrected P-value":0.5006146299996015,
62 "Full adaptive model":0.1241125417707662,
63 "LRT":4.898194538953248,
64 "Nucleotide GTR":0.2481512612523618,
65 "Rate Distributions": [
66 [0, 0.52318726440949],
67 [2.444056517734385, 0.47681273559051]
68 ],
69 "Rate classes":2,
70 "Uncorrected P-value":0.03128841437497509,
71 "original name":"Cow",
72 "rate at which 2 nucleotides are changed instantly within a single codon":0
73 },
74 "Horse":{
75 "Baseline MG94xREV":0.190365915457708,
76 "Baseline MG94xREV omega ratio":1.182933895494305,
77 "Corrected P-value":1,
78 "Full adaptive model":0.0869489794025302,
79 "LRT":2.047309801283518,
80 "Nucleotide GTR":0.2090927256979082,
81 "Rate Distributions": [
82 [0, 0.5397658078247131],
83 [1.633257246666139, 0.4602341921752869]
84 ],
85 "Rate classes":2,
86 "Uncorrected P-value":0.1382789032066179,
87 "original name":"Horse",
88 "rate at which 2 nucleotides are changed instantly within a single codon":0
89 },
90 "Human":{
91 "Baseline MG94xREV":0,
92 "Baseline MG94xREV omega ratio":1,
93 "Corrected P-value":1,
94 "Full adaptive model":0,
95 "LRT":0,
96 "Nucleotide GTR":0,
97 "Rate Distributions": [
98 [1, 1]
99 ],
100 "Rate classes":1,
101 "Uncorrected P-value":1,
102 "original name":"Human",
103 "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574
104 },
105 "Mouse":{
106 "Baseline MG94xREV":0.1083167307250788,
107 "Baseline MG94xREV omega ratio":0.5108576904540283,
108 "Corrected P-value":1,
109 "Full adaptive model":0.1078010043714489,
110 "LRT":0,
111 "Nucleotide GTR":0.1181001275359051,
112 "Rate Distributions": [
113 [0.5087375113796073, 1]
114 ],
115 "Rate classes":1,
116 "Uncorrected P-value":1,
117 "original name":"Mouse",
118 "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548
119 },
120 "Node1":{
121 "Baseline MG94xREV":0.2542393300501047,
122 "Baseline MG94xREV omega ratio":0.2997498382776075,
123 "Corrected P-value":1,
124 "Full adaptive model":0.2550466752020236,
125 "LRT":0,
126 "Nucleotide GTR":0.2767426965701868,
127 "Rate Distributions": [
128 [0.2932817609633239, 1]
129 ],
130 "Rate classes":1,
131 "Uncorrected P-value":1,
132 "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921
133 },
134 "Node12":{
135 "Baseline MG94xREV":0.01400815185374474,
136 "Baseline MG94xREV omega ratio":0.2754467062829232,
137 "Corrected P-value":1,
138 "Full adaptive model":0.01437973904273591,
139 "LRT":0,
140 "Nucleotide GTR":0.01784721909304638,
141 "Rate Distributions": [
142 [0.3037614070859027, 1]
143 ],
144 "Rate classes":1,
145 "Uncorrected P-value":1,
146 "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814
147 },
148 "Node2":{
149 "Baseline MG94xREV":0.0400106272595141,
150 "Baseline MG94xREV omega ratio":0.116408812566168,
151 "Corrected P-value":1,
152 "Full adaptive model":0.03991940069030483,
153 "LRT":0,
154 "Nucleotide GTR":0.06613304839358287,
155 "Rate Distributions": [
156 [0.1193993042178124, 1]
157 ],
158 "Rate classes":1,
159 "Uncorrected P-value":1,
160 "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
161 },
162 "Node3":{
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164 "Baseline MG94xREV omega ratio":1.293385437932658,
165 "Corrected P-value":1,
166 "Full adaptive model":0.08590119038008139,
167 "LRT":0.1383887036890883,
168 "Nucleotide GTR":0.09881178513658169,
169 "Rate Distributions": [
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171 ],
172 "Rate classes":1,
173 "Uncorrected P-value":0.4219212196398351,
174 "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
175 },
176 "Node8":{
177 "Baseline MG94xREV":0.09463393920061362,
178 "Baseline MG94xREV omega ratio":1.862136443854597,
179 "Corrected P-value":1,
180 "Full adaptive model":0.0958035263641453,
181 "LRT":0.7150293976401372,
182 "Nucleotide GTR":0.1062333225692588,
183 "Rate Distributions": [
184 [1.883870769808856, 1]
185 ],
186 "Rate classes":1,
187 "Uncorrected P-value":0.2893795680778183,
188 "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092
189 },
190 "Node9":{
191 "Baseline MG94xREV":0.02846111726225027,
192 "Baseline MG94xREV omega ratio":0.4321055128385307,
193 "Corrected P-value":1,
194 "Full adaptive model":0.02810856974543091,
195 "LRT":0,
196 "Nucleotide GTR":0.02566185438854229,
197 "Rate Distributions": [
198 [0.4185836885800617, 1]
199 ],
200 "Rate classes":1,
201 "Uncorrected P-value":1,
202 "rate at which 2 nucleotides are changed instantly within a single codon":0
203 },
204 "Pig":{
205 "Baseline MG94xREV":0.1782835053555321,
206 "Baseline MG94xREV omega ratio":1.275728452678247,
207 "Corrected P-value":1,
208 "Full adaptive model":0.1729188354138871,
209 "LRT":0.3324036585026988,
210 "Nucleotide GTR":0.1871760137183495,
211 "Rate Distributions": [
212 [1.235108129487059, 1]
213 ],
214 "Rate classes":1,
215 "Uncorrected P-value":0.3669120164240152,
216 "original name":"Pig",
217 "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695
218 },
219 "Rat":{
220 "Baseline MG94xREV":0.06315403896300904,
221 "Baseline MG94xREV omega ratio":0.8744850915248316,
222 "Corrected P-value":1,
223 "Full adaptive model":0.06408078523886611,
224 "LRT":0,
225 "Nucleotide GTR":0.0666364425850592,
226 "Rate Distributions": [
227 [0.8782045320352186, 1]
228 ],
229 "Rate classes":1,
230 "Uncorrected P-value":1,
231 "original name":"Rat",
232 "rate at which 2 nucleotides are changed instantly within a single codon":0.1346164190615118
233 },
234 "RhMonkey":{
235 "Baseline MG94xREV":0.003671939837747083,
236 "Baseline MG94xREV omega ratio":10000000000,
237 "Corrected P-value":1,
238 "Full adaptive model":0.003675047654636179,
239 "LRT":1.165062770327495,
240 "Nucleotide GTR":0.003777016173741061,
241 "Rate Distributions": [
242 [10000000000, 1]
243 ],
244 "Rate classes":1,
245 "Uncorrected P-value":0.2236284592802686,
246 "original name":"RhMonkey",
247 "rate at which 2 nucleotides are changed instantly within a single codon":0
248 }
249 },
250 "attributes":{
251 "Baseline MG94xREV":{
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":{
260 "attribute type":"branch label",
261 "display order":6
262 },
263 "Full adaptive model":{
264 "attribute type":"branch length",
265 "display order":2
266 },
267 "LRT":{
268 "attribute type":"branch label",
269 "display order":4
270 },
271 "Nucleotide GTR":{
272 "attribute type":"branch length",
273 "display order":0
274 },
275 "Rate Distributions":{
276 "attribute type":"branch label",
277 "display order":3
278 },
279 "Rate classes":{
280 "attribute type":"branch label",
281 "display order":2
282 },
283 "Uncorrected P-value":{
284 "attribute type":"branch label",
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":{
306 "Baseline MG94xREV":{
307 "AIC-c":6983.763305606333,
308 "Equilibrium frequencies": [
309 [0.04875339327772683],
310 [0.03982858547830345],
311 [0.04946803524790992],
312 [0.04152216138298744],
313 [0.01811683453600613],
314 [0.01480036248560469],
315 [0.0183823965708893],
316 [0.01542969784826435],
317 [0.01894694796506697],
318 [0.01547851515238824],
319 [0.01922467805342367],
320 [0.01613668666381816],
321 [0.02832099415740372],
322 [0.02313654621336914],
323 [0.02873613184734657],
324 [0.02412034959764736],
325 [0.01662182431200483],
326 [0.01357902918971745],
327 [0.01686547203528639],
328 [0.01415643148428886],
329 [0.006176695005242439],
330 [0.005045987744654046],
331 [0.006267234867003878],
332 [0.005260551308914496],
333 [0.006459711194459957],
334 [0.005277194922783805],
335 [0.006554399593040238],
336 [0.005501589790395056],
337 [0.009655668202293983],
338 [0.007888099278638223],
339 [0.009797203904398108],
340 [0.008223514024394991],
341 [0.03326722643528176],
342 [0.02717732003095303],
343 [0.03375486749252685],
344 [0.02833294365668738],
345 [0.01236215156074466],
346 [0.01009913314808799],
347 [0.01254335971371867],
348 [0.01052856463184265],
349 [0.01292858539344675],
350 [0.0105618754683007],
351 [0.0131180965046964],
352 [0.01101098350431497],
353 [0.0193250328267319],
354 [0.01578738770911659],
355 [0.0196083049972345],
356 [0.01645869298147252],
357 [0.01962343746171723],
358 [0.02045785777700414],
359 [0.008926115885166477],
360 [0.007292098982657142],
361 [0.009056957588961733],
362 [0.007602170831388156],
363 [0.007626222986467745],
364 [0.009471947420992787],
365 [0.007950502328516303],
366 [0.01395367801862353],
367 [0.01139931439306339],
368 [0.01415821524731906],
369 [0.01188403168729233]
370 ],
371 "Log Likelihood":-3427.720059001285,
372 "Rate Distributions":{
373 "Per-branch delta":{
374 "2.5%":0,
375 "97.5%":12.07373117808175,
376 "Mean":1.277646334033236,
377 "Median":0.4551223038316586
378 },
379 "Per-branch omega":{
380 "2.5%":0,
381 "97.5%":2.153434974462683,
382 "Mean":666666667.5119981,
383 "Median":1
384 }
385 },
386 "display order":1,
387 "estimated parameters":62
388 },
389 "Full adaptive model":{
390 "AIC-c":6972.859938351839,
391 "Log Likelihood":-3415.824749853321,
392 "Rate Distributions":{
393 },
394 "display order":2,
395 "estimated parameters":68
396 },
397 "Nucleotide GTR":{
398 "AIC-c":7112.857317645923,
399 "Equilibrium frequencies": [
400 [0.3592490842490842],
401 [0.181959706959707],
402 [0.240018315018315],
403 [0.2187728937728937]
404 ],
405 "Log Likelihood":-3532.321228205235,
406 "Rate Distributions":{
407 "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,
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
413 },
414 "display order":0,
415 "estimated parameters":24
416 }
417 },
418 "input":{
419 "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
420 "number of sequences":10,
421 "number of sites":187,
422 "partition count":1,
423 "trees":{
424 "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)"
425 }
426 },
427 "test results":{
428 "P-value threshold":0.05,
429 "positive test results":0,
430 "tested":16
431 },
432 "tested":{
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",
445 "Node8":"test",
446 "Node9":"test",
447 "Pig":"test",
448 "Rat":"test",
449 "RhMonkey":"test"
450 }
451 },
452 "timers":{
453 "Baseline model fitting":{
454 "order":2,
455 "timer":17
456 },
457 "Complexity analysis":{
458 "order":3,
459 "timer":110
460 },
461 "Full adaptive model fitting":{
462 "order":4,
463 "timer":20
464 },
465 "Overall":{
466 "order":0,
467 "timer":259
468 },
469 "Preliminary model fitting":{
470 "order":1,
471 "timer":0
472 },
473 "Testing for selection":{
474 "order":5,
475 "timer":112
476 }
477 }
478 }