Mercurial > repos > iuc > hyphy_annotate

comparison test-data/relax-out1.json @ 12:6efabd37807b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:44:41 +0000
parents d088a1cca4a7
children
comparison
equal deleted inserted replaced
11:d088a1cca4a7 12:6efabd37807b
1 {
2 "analysis":0,
3 "branch attributes":{
4 "0":{
5 "Baboon":{
6 "General descriptive":0.001859058366368826,
7 "MG94xREV with separate rates for branch sets":0.001769294089885709,
8 "Nucleotide GTR":0.001685167654714891,
9 "RELAX alternative":0.001873708670384941,
10 "RELAX null":0.001859167714920677,
11 "RELAX partitioned descriptive":0.001898817195216417,
12 "k (general descriptive)":0.09969742933359635,
13 "original name":"Baboon"
14 },
15 "Cat":{
16 "General descriptive":0.3650161006190072,
17 "MG94xREV with separate rates for branch sets":0.2796018473093496,
18 "Nucleotide GTR":0.2660536011315811,
19 "RELAX alternative":0.3685874431614762,
20 "RELAX null":0.3167334440346762,
21 "RELAX partitioned descriptive":0.3719472357609613,
22 "k (general descriptive)":2.319877215422834,
23 "original name":"Cat"
24 },
25 "Chimp":{
26 "General descriptive":0.001895983937468787,
27 "MG94xREV with separate rates for branch sets":0.001826027667597702,
28 "Nucleotide GTR":0.001820258053351119,
29 "RELAX alternative":0.001831530791728368,
30 "RELAX null":0.001834052740714585,
31 "RELAX partitioned descriptive":0.001832682515795942,
32 "k (general descriptive)":5.158328270628251,
33 "original name":"Chimp"
34 },
35 "Cow":{
36 "General descriptive":0.3737128696500712,
37 "MG94xREV with separate rates for branch sets":0.2521304147607955,
38 "Nucleotide GTR":0.2480198736772598,
39 "RELAX alternative":0.3426997068768813,
40 "RELAX null":0.2931467439343907,
41 "RELAX partitioned descriptive":0.3469082289876269,
42 "k (general descriptive)":2.852150041266453,
43 "original name":"Cow"
44 },
45 "Horse":{
46 "General descriptive":0.2804279827409984,
47 "MG94xREV with separate rates for branch sets":0.2158535884657318,
48 "Nucleotide GTR":0.2090998951755368,
49 "RELAX alternative":0.3058441352816696,
50 "RELAX null":0.2546949756245578,
51 "RELAX partitioned descriptive":0.3035514182923183,
52 "k (general descriptive)":1.929916608813313,
53 "original name":"Horse"
54 },
55 "Human":{
56 "General descriptive":0,
57 "MG94xREV with separate rates for branch sets":0,
58 "Nucleotide GTR":0,
59 "RELAX alternative":0,
60 "RELAX null":0,
61 "RELAX partitioned descriptive":0,
62 "k (general descriptive)":1.485684693044203,
63 "original name":"Human"
64 },
65 "Mouse":{
66 "General descriptive":0.1308809509233143,
67 "MG94xREV with separate rates for branch sets":0.1197584101055861,
68 "Nucleotide GTR":0.1181058300538561,
69 "RELAX alternative":0.1346294129227689,
70 "RELAX null":0.1438267359449897,
71 "RELAX partitioned descriptive":0.148454172127534,
72 "k (general descriptive)":0.4625550584398252,
73 "original name":"Mouse"
74 },
75 "Node1":{
76 "General descriptive":0.3500691487967139,
77 "MG94xREV with separate rates for branch sets":0.2856782993656827,
78 "Nucleotide GTR":0.2767105173979571,
79 "RELAX alternative":0.385503346940632,
80 "RELAX null":0.4352096867868785,
81 "RELAX partitioned descriptive":0.4379872513902164,
82 "k (general descriptive)":0.4572754180074107
83 },
84 "Node12":{
85 "General descriptive":0.01767932040676307,
86 "MG94xREV with separate rates for branch sets":0.01800350744117403,
87 "Nucleotide GTR":0.01784222107494562,
88 "RELAX alternative":0.01834159481548459,
89 "RELAX null":0.01822563245625142,
90 "RELAX partitioned descriptive":0.01881534539472323,
91 "k (general descriptive)":0.1240073621579099
92 },
93 "Node2":{
94 "General descriptive":0.05767151047612454,
95 "MG94xREV with separate rates for branch sets":0.06170856993599769,
96 "Nucleotide GTR":0.06614755778044307,
97 "RELAX alternative":0.0544792799094392,
98 "RELAX null":0.06013052353393462,
99 "RELAX partitioned descriptive":0.0601550105387935,
100 "k (general descriptive)":0.5400834620465133
101 },
102 "Node3":{
103 "General descriptive":0.1330088052861041,
104 "MG94xREV with separate rates for branch sets":0.09733132151710643,
105 "Nucleotide GTR":0.09883748387954429,
106 "RELAX alternative":0.1169235247351394,
107 "RELAX null":0.1263887172366205,
108 "RELAX partitioned descriptive":0.1196402015693241,
109 "k (general descriptive)":1.977892771876671
110 },
111 "Node8":{
112 "General descriptive":0.140412283431793,
113 "MG94xREV with separate rates for branch sets":0.1091939823455765,
114 "Nucleotide GTR":0.1062201244057951,
115 "RELAX alternative":0.1284192265733904,
116 "RELAX null":0.1334227466998376,
117 "RELAX partitioned descriptive":0.1367904558404228,
118 "k (general descriptive)":2.206967022203622
119 },
120 "Node9":{
121 "General descriptive":0.02664133794298214,
122 "MG94xREV with separate rates for branch sets":0.02578742148415842,
123 "Nucleotide GTR":0.02567813733543303,
124 "RELAX alternative":0.02680940150436639,
125 "RELAX null":0.0273694783141817,
126 "RELAX partitioned descriptive":0.02747376898615263,
127 "k (general descriptive)":0.07343731037788495
128 },
129 "Pig":{
130 "General descriptive":0.210591346560755,
131 "MG94xREV with separate rates for branch sets":0.1903463787974325,
132 "Nucleotide GTR":0.1871390433004313,
133 "RELAX alternative":0.1974790507889271,
134 "RELAX null":0.2130024973755621,
135 "RELAX partitioned descriptive":0.2084407457285946,
136 "k (general descriptive)":1.581210670484469,
137 "original name":"Pig"
138 },
139 "Rat":{
140 "General descriptive":0.07157977734335202,
141 "MG94xREV with separate rates for branch sets":0.06709765698107663,
142 "Nucleotide GTR":0.06661490534189227,
143 "RELAX alternative":0.07252374836036582,
144 "RELAX null":0.0734705682786943,
145 "RELAX partitioned descriptive":0.0757525093290258,
146 "k (general descriptive)":1.316568267879453,
147 "original name":"Rat"
148 },
149 "RhMonkey":{
150 "General descriptive":0.003672848089716511,
151 "MG94xREV with separate rates for branch sets":0.003717350789869306,
152 "Nucleotide GTR":0.003778804730491441,
153 "RELAX alternative":0.003633278464154418,
154 "RELAX null":0.003661271320845124,
155 "RELAX partitioned descriptive":0.003625957794514879,
156 "k (general descriptive)":5.196295069596697,
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":{
204 "General descriptive":{
205 "AIC-c":6945.892677835464,
206 "Log Likelihood":-3420.487593043145,
207 "Rate Distributions":{
208 "Shared":{
209 "0":{
210 "omega":2.201451464048879e-18,
211 "proportion":0.3073650505039141
212 },
213 "1":{
214 "omega":2.201451464048879e-18,
215 "proportion":0.2383891488636319
216 },
217 "2":{
218 "omega":2.201451281679838,
219 "proportion":0.4542458006324541
220 }
221 }
222 },
223 "display order":4,
224 "estimated parameters":51
225 },
226 "MG94xREV with separate rates for branch sets":{
227 "AIC-c":6987.566513560764,
228 "Equilibrium frequencies": [
229 [0.04876086397632926],
230 [0.03982224127745371],
231 [0.0494959405650269],
232 [0.04152830682371345],
233 [0.01810345074594235],
234 [0.01478480742075003],
235 [0.01837636270304883],
236 [0.01541821854326533],
237 [0.01892910005547028],
238 [0.01545910240515689],
239 [0.01921445878706794],
240 [0.01612140169177368],
241 [0.02829747763884322],
242 [0.02311011106415996],
243 [0.02872406592369408],
244 [0.02410019507229243],
245 [0.01663805943190806],
246 [0.01358804506433061],
247 [0.01688888041768248],
248 [0.01417018446135155],
249 [0.006177213955434187],
250 [0.005044834822351987],
251 [0.006270336287397383],
252 [0.00526096577332031],
253 [0.006458939937330408],
254 [0.005274916061901906],
255 [0.006556309326397028],
256 [0.005500904159606446],
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":-3461.208406480981,
292 "Rate Distributions":{
293 "non-synonymous/synonymous rate ratio for *Reference*": [
294 [0.7685912547191639, 1]
295 ],
296 "non-synonymous/synonymous rate ratio for *Test*": [
297 [1.603198088111489, 1]
298 ]
299 },
300 "display order":1,
301 "estimated parameters":32
302 },
303 "Nucleotide GTR":{
304 "AIC-c":7112.857288723968,
305 "Equilibrium frequencies": [
306 [0.3592490842490842],
307 [0.181959706959707],
308 [0.240018315018315],
309 [0.2187728937728937]
310 ],
311 "Log Likelihood":-3532.321213744258,
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":0.2646800222727828,
316 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
317 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
318 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
319 },
320 "display order":0,
321 "estimated parameters":24
322 },
323 "RELAX alternative":{
324 "AIC-c":6931.926773483473,
325 "Log Likelihood":-3429.236709163995,
326 "Rate Distributions":{
327 "Reference":{
328 "0":{
329 "omega":1.761161171239182e-19,
330 "proportion":0.2691773911207853
331 },
332 "1":{
333 "omega":1.762922332410267e-19,
334 "proportion":0.2692122656891806
335 },
336 "2":{
337 "omega":2.208286837998088,
338 "proportion":0.4616103431900341
339 }
340 },
341 "Test":{
342 "0":{
343 "omega":1.673670300056362e-44,
344 "proportion":0.2691773911207853
345 },
346 "1":{
347 "omega":1.677579612236672e-44,
348 "proportion":0.2692122656891806
349 },
350 "2":{
351 "omega":6.354762788556926,
352 "proportion":0.4616103431900341
353 }
354 }
355 },
356 "display order":2,
357 "estimated parameters":36
358 },
359 "RELAX null":{
360 "AIC-c":6946.648596594286,
361 "Log Likelihood":-3437.63727539638,
362 "Rate Distributions":{
363 "Reference":{
364 "0":{
365 "omega":1.408928936991542e-20,
366 "proportion":0.265244047162938
367 },
368 "1":{
369 "omega":1.410337865928411e-20,
370 "proportion":0.28512630848952
371 },
372 "2":{
373 "omega":3.213510017765925,
374 "proportion":0.4496296443475419
375 }
376 },
377 "Test":{
378 "0":{
379 "omega":1.408928936991542e-20,
380 "proportion":0.265244047162938
381 },
382 "1":{
383 "omega":1.410337865928411e-20,
384 "proportion":0.28512630848952
385 },
386 "2":{
387 "omega":3.213510017765925,
388 "proportion":0.4496296443475419
389 }
390 }
391 },
392 "display order":3,
393 "estimated parameters":35
394 },
395 "RELAX partitioned descriptive":{
396 "AIC-c":6937.049237937651,
397 "Log Likelihood":-3427.627954124649,
398 "Rate Distributions":{
399 "Reference":{
400 "0":{
401 "omega":0.1847557016619168,
402 "proportion":0.4766160247339328
403 },
404 "1":{
405 "omega":0.3367540359539261,
406 "proportion":0.3005513276312735
407 },
408 "2":{
409 "omega":4.272816072857538,
410 "proportion":0.2228326476347937
411 }
412 },
413 "Test":{
414 "0":{
415 "omega":1.127143149593234e-21,
416 "proportion":0.2367540589657237
417 },
418 "1":{
419 "omega":1.128270292740756e-21,
420 "proportion":0.2771164325302933
421 },
422 "2":{
423 "omega":6.023626417874829,
424 "proportion":0.4861295085039831
425 }
426 }
427 },
428 "display order":5,
429 "estimated parameters":40
430 }
431 },
432 "input":{
433 "file name":"/tmp/tmpkgsdjj1d/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 "runtime":"2.5.32",
442 "test results":{
443 "LRT":16.80113246476958,
444 "p-value":4.150852429507523e-05,
445 "relaxation or intensification parameter":2.334214628944839
446 },
447 "tested":{
448 "0":{
449 "Baboon":"Reference",
450 "Cat":"Test",
451 "Chimp":"Reference",
452 "Cow":"Test",
453 "Horse":"Test",
454 "Human":"Reference",
455 "Mouse":"Reference",
456 "Node1":"Reference",
457 "Node12":"Reference",
458 "Node2":"Reference",
459 "Node3":"Reference",
460 "Node8":"Reference",
461 "Node9":"Reference",
462 "Pig":"Reference",
463 "Rat":"Reference",
464 "RhMonkey":"Reference"
465 }
466 },
467 "timers":{
468 "General descriptive model fitting":{
469 "order":2,
470 "timer":127
471 },
472 "Overall":{
473 "order":0,
474 "timer":396
475 },
476 "Preliminary model fitting":{
477 "order":1,
478 "timer":8
479 },
480 "RELAX alternative model fitting":{
481 "order":3,
482 "timer":103
483 },
484 "RELAX null model fitting":{
485 "order":4,
486 "timer":41
487 },
488 "RELAX partitioned descriptive":{
489 "order":5,
490 "timer":116
491 }
492 }
493 }