Mercurial > repos > iuc > hyphy_summary

comparison test-data/relax-out1.json @ 0:f304c108aa1f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:03:54 +0000
parents
children 81b23515db14
comparison
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-1:000000000000 0:f304c108aa1f
1 {
2 "analysis":0,
3 "branch attributes":{
4 "0":{
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7 "MG94xREV with separate rates for branch sets":0.001769472024099301,
8 "Nucleotide GTR":0.001680040630127455,
9 "RELAX alternative":0.001872256662230973,
10 "RELAX null":0.001855569334462731,
11 "RELAX partitioned descriptive":0.001898170574782418,
12 "k (general descriptive)":0.09971581394819819,
13 "original name":"Baboon"
14 },
15 "Cat":{
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22 "k (general descriptive)":2.314507643873676,
23 "original name":"Cat"
24 },
25 "Chimp":{
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27 "MG94xREV with separate rates for branch sets":0.001825434296531533,
28 "Nucleotide GTR":0.001818373670119325,
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31 "RELAX partitioned descriptive":0.001832717232153088,
32 "k (general descriptive)":5.261186652622472,
33 "original name":"Chimp"
34 },
35 "Cow":{
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43 "original name":"Cow"
44 },
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63 "original name":"Human"
64 },
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73 "original name":"Mouse"
74 },
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110 },
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129 "Pig":{
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137 "original name":"Pig"
138 },
139 "Rat":{
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146 "k (general descriptive)":1.318174884032695,
147 "original name":"Rat"
148 },
149 "RhMonkey":{
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156 "k (general descriptive)":5.171610533872274,
157 "original name":"RhMonkey"
158 }
159 },
160 "attributes":{
161 "General descriptive":{
162 "attribute type":"branch length",
163 "display order":4
164 },
165 "MG94xREV with separate rates for branch sets":{
166 "attribute type":"branch length",
167 "display order":1
168 },
169 "Nucleotide GTR":{
170 "attribute type":"branch length",
171 "display order":0
172 },
173 "RELAX alternative":{
174 "attribute type":"branch length",
175 "display order":2
176 },
177 "RELAX null":{
178 "attribute type":"branch length",
179 "display order":3
180 },
181 "RELAX partitioned descriptive":{
182 "attribute type":"branch length",
183 "display order":5
184 },
185 "k (general descriptive)":{
186 "attribute type":"branch label",
187 "display order":4
188 },
189 "original name":{
190 "attribute type":"node label",
191 "display order":-1
192 }
193 }
194 },
195 "data partitions":{
196 "0":{
197 "coverage": [
198 [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]
199 ],
200 "name":"relax.filter.default"
201 }
202 },
203 "fits":{
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206 "Log Likelihood":-3420.486931066253,
207 "Rate Distributions":{
208 "Shared":{
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213 "1":{
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219 "proportion":0.4539604211125504
220 }
221 }
222 },
223 "display order":4,
224 "estimated parameters":51
225 },
226 "MG94xREV with separate rates for branch sets":{
227 "AIC-c":6987.565999172035,
228 "Equilibrium frequencies": [
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230 [0.03982224127745371],
231 [0.0494959405650269],
232 [0.04152830682371345],
233 [0.01810345074594235],
234 [0.01478480742075003],
235 [0.01837636270304883],
236 [0.01541821854326533],
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238 [0.01545910240515689],
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252 [0.00526096577332031],
253 [0.006458939937330408],
254 [0.005274916061901906],
255 [0.006556309326397028],
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257 [0.009655594186286731],
258 [0.007885574003572761],
259 [0.009801153568494354],
260 [0.008223407979974132],
261 [0.03327785448210915],
262 [0.02717750758119989],
263 [0.03377952261833742],
264 [0.02834184710178207],
265 [0.01235507229404208],
266 [0.01009019590244688],
267 [0.01254132667213156],
268 [0.01052248035033209],
269 [0.01291855364640413],
270 [0.01055038238273567],
271 [0.01311330258173711],
272 [0.01100238215235291],
273 [0.01931219560697892],
274 [0.0157719705998612],
275 [0.01960332955558842],
276 [0.01644767379420349],
277 [0.01965132601881859],
278 [0.02049322866376102],
279 [0.008933621043463411],
280 [0.007295949736387736],
281 [0.009068296583349953],
282 [0.007608523013862737],
283 [0.007628698224327205],
284 [0.009481877006094248],
285 [0.00795552712159237],
286 [0.01396413011303752],
287 [0.01140428846505027],
288 [0.01417464125436193],
289 [0.01189287130232129]
290 ],
291 "Log Likelihood":-3461.208149286616,
292 "Rate Distributions":{
293 "non-synonymous/synonymous rate ratio for *Reference*": [
294 [0.7682335289209781, 1]
295 ],
296 "non-synonymous/synonymous rate ratio for *Test*": [
297 [1.605439824256426, 1]
298 ]
299 },
300 "display order":1,
301 "estimated parameters":32
302 },
303 "Nucleotide GTR":{
304 "AIC-c":7112.857310169033,
305 "Equilibrium frequencies": [
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307 [0.181959706959707],
308 [0.240018315018315],
309 [0.2187728937728937]
310 ],
311 "Log Likelihood":-3532.32122446679,
312 "Rate Distributions":{
313 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
314 "Substitution rate from nucleotide A to nucleotide G":1,
315 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
316 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
317 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
318 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
319 },
320 "display order":0,
321 "estimated parameters":24
322 },
323 "RELAX alternative":{
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325 "Log Likelihood":-3429.234812770952,
326 "Rate Distributions":{
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330 "proportion":0.4504132080156107
331 },
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339 }
340 },
341 "Test":{
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344 "proportion":0.4504132080156107
345 },
346 "1":{
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348 "proportion":0.08749553114962015
349 },
350 "2":{
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352 "proportion":0.4620912608347691
353 }
354 }
355 },
356 "display order":2,
357 "estimated parameters":36
358 },
359 "RELAX null":{
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361 "Log Likelihood":-3437.336313352972,
362 "Rate Distributions":{
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366 "proportion":0.542405144031307
367 },
368 "1":{
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370 "proportion":0.08223353569636478
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372 "2":{
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374 "proportion":0.3753613202723282
375 }
376 },
377 "Test":{
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380 "proportion":0.542405144031307
381 },
382 "1":{
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384 "proportion":0.08223353569636478
385 },
386 "2":{
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388 "proportion":0.3753613202723282
389 }
390 }
391 },
392 "display order":3,
393 "estimated parameters":35
394 },
395 "RELAX partitioned descriptive":{
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397 "Log Likelihood":-3427.626871923648,
398 "Rate Distributions":{
399 "Reference":{
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402 "proportion":0.3359458135547653
403 },
404 "1":{
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406 "proportion":0.4332550437039296
407 },
408 "2":{
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410 "proportion":0.2307991427413052
411 }
412 },
413 "Test":{
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416 "proportion":0.4753488415962343
417 },
418 "1":{
419 "omega":0,
420 "proportion":0.03858318603767072
421 },
422 "2":{
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424 "proportion":0.486067972366095
425 }
426 }
427 },
428 "display order":5,
429 "estimated parameters":40
430 }
431 },
432 "input":{
433 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",
434 "number of sequences":10,
435 "number of sites":187,
436 "partition count":1,
437 "trees":{
438 "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)"
439 }
440 },
441 "test results":{
442 "LRT":16.20300116404087,
443 "p-value":5.690389451429301e-05,
444 "relaxation or intensification parameter":2.344938789085876
445 },
446 "tested":{
447 "0":{
448 "Baboon":"Reference",
449 "Cat":"Test",
450 "Chimp":"Reference",
451 "Cow":"Test",
452 "Horse":"Test",
453 "Human":"Reference",
454 "Mouse":"Reference",
455 "Node1":"Reference",
456 "Node12":"Reference",
457 "Node2":"Reference",
458 "Node3":"Reference",
459 "Node8":"Reference",
460 "Node9":"Reference",
461 "Pig":"Reference",
462 "Rat":"Reference",
463 "RhMonkey":"Reference"
464 }
465 },
466 "timers":{
467 "General descriptive model fitting":{
468 "order":2,
469 "timer":132
470 },
471 "Overall":{
472 "order":0,
473 "timer":324
474 },
475 "Preliminary model fitting":{
476 "order":1,
477 "timer":8
478 },
479 "RELAX alternative model fitting":{
480 "order":3,
481 "timer":65
482 },
483 "RELAX null model fitting":{
484 "order":4,
485 "timer":66
486 },
487 "RELAX partitioned descriptive":{
488 "order":5,
489 "timer":53
490 }
491 }
492 }