Mercurial > repos > iuc > hyphy_bgm

comparison test-data/relax-out2-1.json @ 25:d88bbb287923 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:01:09 +0000
parents
children 5b6b8b08f1a9
comparison
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24:e14d926dfdc4 25:d88bbb287923
1 {
2 "Synonymous site-posteriors": [
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150 "RELAX partitioned descriptive":0.07467247582140474,
151 "k (general descriptive)":1.319839560623237,
152 "original name":"RAT"
153 },
154 "RHMONKEY":{
155 "General descriptive":0.003674114425886965,
156 "MG94xREV with separate rates for branch sets":0.003753885794232333,
157 "Nucleotide GTR":0.003775170135617877,
158 "RELAX alternative":0.004180662465434332,
159 "RELAX null":0.003978610819466039,
160 "RELAX partitioned descriptive":0.004190519057865823,
161 "k (general descriptive)":5.183560186695944,
162 "original name":"RHMONKEY"
163 }
164 },
165 "attributes":{
166 "General descriptive":{
167 "attribute type":"branch length",
168 "display order":4
169 },
170 "MG94xREV with separate rates for branch sets":{
171 "attribute type":"branch length",
172 "display order":1
173 },
174 "Nucleotide GTR":{
175 "attribute type":"branch length",
176 "display order":0
177 },
178 "RELAX alternative":{
179 "attribute type":"branch length",
180 "display order":2
181 },
182 "RELAX null":{
183 "attribute type":"branch length",
184 "display order":3
185 },
186 "RELAX partitioned descriptive":{
187 "attribute type":"branch length",
188 "display order":5
189 },
190 "k (general descriptive)":{
191 "attribute type":"branch label",
192 "display order":4
193 },
194 "original name":{
195 "attribute type":"node label",
196 "display order":-1
197 }
198 }
199 },
200 "data partitions":{
201 "0":{
202 "coverage": [
203 [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]
204 ],
205 "name":"relax.filter.default"
206 }
207 },
208 "fits":{
209 "General descriptive":{
210 "AIC-c":6945.891070751259,
211 "Log Likelihood":-3420.486789501042,
212 "Rate Distributions":{
213 "Shared":{
214 "0":{
215 "omega":2.20271427504516e-18,
216 "proportion":0.00789425874100967
217 },
218 "1":{
219 "omega":2.20271427504516e-18,
220 "proportion":0.5381203586928067
221 },
222 "2":{
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224 "proportion":0.4539853825661836
225 }
226 }
227 },
228 "display order":4,
229 "estimated parameters":51
230 },
231 "MG94xREV with separate rates for branch sets":{
232 "AIC-c":6987.278662183248,
233 "Equilibrium frequencies": [
234 [0.04876086397632926],
235 [0.03982224127745371],
236 [0.0494959405650269],
237 [0.04152830682371345],
238 [0.01810345074594235],
239 [0.01478480742075003],
240 [0.01837636270304883],
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242 [0.01892910005547028],
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244 [0.01921445878706794],
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246 [0.02829747763884322],
247 [0.02311011106415996],
248 [0.02872406592369408],
249 [0.02410019507229243],
250 [0.01663805943190806],
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253 [0.01417018446135155],
254 [0.006177213955434187],
255 [0.005044834822351987],
256 [0.006270336287397383],
257 [0.00526096577332031],
258 [0.006458939937330408],
259 [0.005274916061901906],
260 [0.006556309326397028],
261 [0.005500904159606446],
262 [0.009655594186286731],
263 [0.007885574003572761],
264 [0.009801153568494354],
265 [0.008223407979974132],
266 [0.03327785448210915],
267 [0.02717750758119989],
268 [0.03377952261833742],
269 [0.02834184710178207],
270 [0.01235507229404208],
271 [0.01009019590244688],
272 [0.01254132667213156],
273 [0.01052248035033209],
274 [0.01291855364640413],
275 [0.01055038238273567],
276 [0.01311330258173711],
277 [0.01100238215235291],
278 [0.01931219560697892],
279 [0.0157719705998612],
280 [0.01960332955558842],
281 [0.01644767379420349],
282 [0.01965132601881859],
283 [0.02049322866376102],
284 [0.008933621043463411],
285 [0.007295949736387736],
286 [0.009068296583349953],
287 [0.007608523013862737],
288 [0.007628698224327205],
289 [0.009481877006094248],
290 [0.00795552712159237],
291 [0.01396413011303752],
292 [0.01140428846505027],
293 [0.01417464125436193],
294 [0.01189287130232129]
295 ],
296 "Log Likelihood":-3461.064480792223,
297 "Rate Distributions":{
298 "non-synonymous/synonymous rate ratio for *Reference*": [
299 [1.240656122625563, 1]
300 ],
301 "non-synonymous/synonymous rate ratio for *Test*": [
302 [0.5611761689874598, 1]
303 ]
304 },
305 "display order":1,
306 "estimated parameters":32
307 },
308 "Nucleotide GTR":{
309 "AIC-c":7112.857310169033,
310 "Equilibrium frequencies": [
311 [0.3592490842490842],
312 [0.181959706959707],
313 [0.240018315018315],
314 [0.2187728937728937]
315 ],
316 "Log Likelihood":-3532.32122446679,
317 "Rate Distributions":{
318 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
319 "Substitution rate from nucleotide A to nucleotide G":1,
320 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
321 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
322 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
323 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
324 },
325 "display order":0,
326 "estimated parameters":24
327 },
328 "RELAX alternative":{
329 "AIC-c":6901.392449196474,
330 "Log Likelihood":-3408.754211469135,
331 "Rate Distributions":{
332 "Reference":{
333 "0":{
334 "omega":0,
335 "proportion":0.3814061972635792
336 },
337 "1":{
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339 "proportion":0
340 },
341 "2":{
342 "omega":2.405594515133199,
343 "proportion":0.6185938027364208
344 }
345 },
346 "Synonymous site-to-site rates":{
347 "0":{
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349 "rate":0.2837970682663188
350 },
351 "1":{
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353 "rate":0.9947075941569237
354 },
355 "2":{
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357 "rate":3.20135608237551
358 }
359 },
360 "Test":{
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363 "proportion":0.3814061972635792
364 },
365 "1":{
366 "omega":0.9999750044281671,
367 "proportion":0
368 },
369 "2":{
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371 "proportion":0.6185938027364208
372 }
373 }
374 },
375 "display order":2,
376 "estimated parameters":41
377 },
378 "RELAX null":{
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380 "Log Likelihood":-3414.491942969586,
381 "Rate Distributions":{
382 "Reference":{
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385 "proportion":0.04600287725570656
386 },
387 "1":{
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389 "proportion":0.3432466763494891
390 },
391 "2":{
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393 "proportion":0.6107504463948045
394 }
395 },
396 "Synonymous site-to-site rates":{
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399 "rate":0.2744837794048847
400 },
401 "1":{
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403 "rate":0.9729462345446451
404 },
405 "2":{
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407 "rate":3.029415427453047
408 }
409 },
410 "Test":{
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413 "proportion":0.04600287725570656
414 },
415 "1":{
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417 "proportion":0.3432466763494891
418 },
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421 "proportion":0.6107504463948045
422 }
423 }
424 },
425 "display order":3,
426 "estimated parameters":40
427 },
428 "RELAX partitioned descriptive":{
429 "AIC-c":6909.42794543134,
430 "Log Likelihood":-3408.579104294618,
431 "Rate Distributions":{
432 "Reference":{
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435 "proportion":0.3805224005150026
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437 "1":{
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441 "2":{
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443 "proportion":0.6160154753212325
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445 },
446 "Test":{
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449 "proportion":0.03160127773820932
450 },
451 "1":{
452 "omega":0,
453 "proportion":0.4079248249859382
454 },
455 "2":{
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457 "proportion":0.5604738972758525
458 }
459 }
460 },
461 "display order":5,
462 "estimated parameters":45
463 }
464 },
465 "input":{
466 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex",
467 "number of sequences":10,
468 "number of sites":187,
469 "partition count":1,
470 "trees":{
471 "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)"
472 }
473 },
474 "test results":{
475 "LRT":11.47546300090198,
476 "p-value":0.0007052107640865835,
477 "relaxation or intensification parameter":2.986519568748539e-05
478 },
479 "tested":{
480 "0":{
481 "BABOON":"Test",
482 "CAT":"Reference",
483 "CHIMP":"Test",
484 "COW":"Reference",
485 "HORSE":"Reference",
486 "HUMAN":"Test",
487 "MOUSE":"Reference",
488 "Node1":"Test",
489 "Node12":"Test",
490 "Node2":"Reference",
491 "Node3":"Reference",
492 "Node8":"Test",
493 "Node9":"Test",
494 "PIG":"Reference",
495 "RAT":"Reference",
496 "RHMONKEY":"Test"
497 }
498 },
499 "timers":{
500 "General descriptive model fitting":{
501 "order":2,
502 "timer":127
503 },
504 "Overall":{
505 "order":0,
506 "timer":645
507 },
508 "Preliminary model fitting":{
509 "order":1,
510 "timer":8
511 },
512 "RELAX alternative model fitting":{
513 "order":3,
514 "timer":178
515 },
516 "RELAX null model fitting":{
517 "order":4,
518 "timer":115
519 },
520 "RELAX partitioned descriptive":{
521 "order":5,
522 "timer":216
523 }
524 }
525 }