Mercurial > repos > iuc > hyphy_absrel
comparison test-data/relax-out1.json @ 1:5c87e4907e08 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author | iuc |
---|---|
date | Wed, 21 Aug 2019 12:24:13 -0400 |
parents | |
children | 5f2ca10db92a |
comparison
equal
deleted
inserted
replaced
0:419cd817299c | 1:5c87e4907e08 |
---|---|
1 { | |
2 "analysis":{ | |
3 "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems", | |
4 "version":"2.1", | |
5 "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832", | |
6 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", | |
7 "contact":"spond@temple.edu", | |
8 "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)" | |
9 }, | |
10 "input":{ | |
11 "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa", | |
12 "number of sequences":10, | |
13 "number of sites":187, | |
14 "partition count":1, | |
15 "trees":{ | |
16 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,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)" | |
17 } | |
18 }, | |
19 "fits":{ | |
20 "Nucleotide GTR":{ | |
21 "Log Likelihood":-3531.964032193222, | |
22 "estimated parameters":24, | |
23 "AIC-c":7112.142925621896, | |
24 "Equilibrium frequencies":[ | |
25 [0.3563279857397504], | |
26 [0.1837789661319073], | |
27 [0.2402852049910873], | |
28 [0.2196078431372549] | |
29 ], | |
30 "Rate Distributions":{ | |
31 "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838, | |
32 "Substitution rate from nucleotide A to nucleotide G":1, | |
33 "Substitution rate from nucleotide A to nucleotide T":0.264131123736109, | |
34 "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388, | |
35 "Substitution rate from nucleotide C to nucleotide T":1.017887589835735, | |
36 "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065 | |
37 }, | |
38 "display order":0 | |
39 }, | |
40 "MG94xREV with separate rates for branch sets":{ | |
41 "Log Likelihood":-3460.931903299487, | |
42 "estimated parameters":32, | |
43 "AIC-c":6987.013507197776, | |
44 "Equilibrium frequencies":[ | |
45 [0.04785168648208005], | |
46 [0.03911346079312019], | |
47 [0.04842054060317301], | |
48 [0.04069665666515385], | |
49 [0.01817010744778396], | |
50 [0.01485205303123071], | |
51 [0.01838611113045968], | |
52 [0.01545321970309948], | |
53 [0.0190138898893362], | |
54 [0.01554175184587827], | |
55 [0.01923992433904378], | |
56 [0.01617083546230154], | |
57 [0.02796925133965702], | |
58 [0.02286176927319543], | |
59 [0.02830174586718859], | |
60 [0.02378714529482007], | |
61 [0.01687870337957799], | |
62 [0.01379647304851128], | |
63 [0.01707935503225849], | |
64 [0.01435491300079667], | |
65 [0.006409133648843443], | |
66 [0.005238757839512795], | |
67 [0.006485324528555602], | |
68 [0.005450807083377185], | |
69 [0.006706760641638982], | |
70 [0.005482034985409045], | |
71 [0.006786489669196017], | |
72 [0.005703931360295163], | |
73 [0.009865581170012171], | |
74 [0.008064021368173151], | |
75 [0.009982861811889655], | |
76 [0.008390428826966174], | |
77 [0.03287895020631181], | |
78 [0.02687490503171972], | |
79 [0.033269810543681], | |
80 [0.0279627207822247], | |
81 [0.01248470225271473], | |
82 [0.01020486315060615], | |
83 [0.01263311863778268], | |
84 [0.01061792547971484], | |
85 [0.01306446616325414], | |
86 [0.01067875601941112], | |
87 [0.01321977470017749], | |
88 [0.01111100011404158], | |
89 [0.01921770557551369], | |
90 [0.01570834862514353], | |
91 [0.01944616295744266], | |
92 [0.01634417558076203], | |
93 [0.01975257768318274], | |
94 [0.02055210293142003], | |
95 [0.009176034326710849], | |
96 [0.007500393094996483], | |
97 [0.00928511773266342], | |
98 [0.007803986567571961], | |
99 [0.00784869593340758], | |
100 [0.009716299514778986], | |
101 [0.008166387662818644], | |
102 [0.01412467213650941], | |
103 [0.01154535713247913], | |
104 [0.01429258425298098], | |
105 [0.01201267864744234] | |
106 ], | |
107 "Rate Distributions":{ | |
108 "non-synonymous/synonymous rate ratio for *Reference*":[ | |
109 [1.617765969026557, 1] | |
110 ], | |
111 "non-synonymous/synonymous rate ratio for *Test*":[ | |
112 [0.7687683974183303, 1] | |
113 ] | |
114 }, | |
115 "display order":1 | |
116 }, | |
117 "General descriptive":{ | |
118 "Log Likelihood":-3420.975369746331, | |
119 "estimated parameters":51, | |
120 "AIC-c":6946.868231241836, | |
121 "Rate Distributions":{ | |
122 "Shared":{ | |
123 "0":{ | |
124 "omega":1e-08, | |
125 "proportion":0.2345034364701236 | |
126 }, | |
127 "1":{ | |
128 "omega":1e-08, | |
129 "proportion":0.3180344596999608 | |
130 }, | |
131 "2":{ | |
132 "omega":6.64943557055033, | |
133 "proportion":0.4474621038299156 | |
134 } | |
135 } | |
136 }, | |
137 "display order":4 | |
138 }, | |
139 "RELAX alternative":{ | |
140 "Log Likelihood":-3429.125323833579, | |
141 "estimated parameters":36, | |
142 "AIC-c":6931.704002822642, | |
143 "Rate Distributions":{ | |
144 "Test":{ | |
145 "0":{ | |
146 "omega":0, | |
147 "proportion":0.1993913071931658 | |
148 }, | |
149 "1":{ | |
150 "omega":0, | |
151 "proportion":0.3360341729181165 | |
152 }, | |
153 "2":{ | |
154 "omega":2.153056268947235, | |
155 "proportion":0.4645745198887177 | |
156 } | |
157 }, | |
158 "Reference":{ | |
159 "0":{ | |
160 "omega":0, | |
161 "proportion":0.1993913071931658 | |
162 }, | |
163 "1":{ | |
164 "omega":0, | |
165 "proportion":0.3360341729181165 | |
166 }, | |
167 "2":{ | |
168 "omega":6.166712663934246, | |
169 "proportion":0.4645745198887177 | |
170 } | |
171 } | |
172 }, | |
173 "display order":2 | |
174 }, | |
175 "RELAX null":{ | |
176 "Log Likelihood":-3437.187429488768, | |
177 "estimated parameters":35, | |
178 "AIC-c":6945.748904779063, | |
179 "Rate Distributions":{ | |
180 "Test":{ | |
181 "0":{ | |
182 "omega":0.1177689533662908, | |
183 "proportion":0.4926494715348529 | |
184 }, | |
185 "1":{ | |
186 "omega":0.3195682613972807, | |
187 "proportion":0.1517366025099117 | |
188 }, | |
189 "2":{ | |
190 "omega":3.893733071412322, | |
191 "proportion":0.3556139259552353 | |
192 } | |
193 }, | |
194 "Reference":{ | |
195 "0":{ | |
196 "omega":0.1177689533662908, | |
197 "proportion":0.4926494715348529 | |
198 }, | |
199 "1":{ | |
200 "omega":0.3195682613972807, | |
201 "proportion":0.1517366025099117 | |
202 }, | |
203 "2":{ | |
204 "omega":3.893733071412322, | |
205 "proportion":0.3556139259552353 | |
206 } | |
207 } | |
208 }, | |
209 "display order":3 | |
210 }, | |
211 "RELAX partitioned descriptive":{ | |
212 "Log Likelihood":-3427.515821600644, | |
213 "estimated parameters":40, | |
214 "AIC-c":6936.824972889643, | |
215 "Rate Distributions":{ | |
216 "Test":{ | |
217 "0":{ | |
218 "omega":0.2264899618249929, | |
219 "proportion":0.1370778077745601 | |
220 }, | |
221 "1":{ | |
222 "omega":0.2328054750512875, | |
223 "proportion":0.6322930022247097 | |
224 }, | |
225 "2":{ | |
226 "omega":4.13407071706127, | |
227 "proportion":0.2306291900007301 | |
228 } | |
229 }, | |
230 "Reference":{ | |
231 "0":{ | |
232 "omega":0, | |
233 "proportion":0.09054841512283768 | |
234 }, | |
235 "1":{ | |
236 "omega":0, | |
237 "proportion":0.4231976237742962 | |
238 }, | |
239 "2":{ | |
240 "omega":5.975493863572218, | |
241 "proportion":0.4862539611028661 | |
242 } | |
243 } | |
244 }, | |
245 "display order":5 | |
246 } | |
247 }, | |
248 "timers":{ | |
249 "Overall":{ | |
250 "timer":562, | |
251 "order":0 | |
252 }, | |
253 "Preliminary model fitting":{ | |
254 "timer":33, | |
255 "order":1 | |
256 }, | |
257 "General descriptive model fitting":{ | |
258 "timer":256, | |
259 "order":2 | |
260 }, | |
261 "RELAX alternative model fitting":{ | |
262 "timer":78, | |
263 "order":3 | |
264 }, | |
265 "RELAX null model fitting":{ | |
266 "timer":98, | |
267 "order":4 | |
268 }, | |
269 "RELAX partitioned descriptive":{ | |
270 "timer":95, | |
271 "order":5 | |
272 } | |
273 }, | |
274 "test results":{ | |
275 "LRT":16.12421131037809, | |
276 "p-value":5.932080525117289e-05, | |
277 "relaxation or intensification parameter":0.4215604262166031 | |
278 }, | |
279 "tested":{ | |
280 "0":{ | |
281 "Pig":"Test", | |
282 "Cow":"Reference", | |
283 "Node3":"Test", | |
284 "Horse":"Reference", | |
285 "Cat":"Reference", | |
286 "Node2":"Test", | |
287 "RhMonkey":"Test", | |
288 "Baboon":"Test", | |
289 "Node9":"Test", | |
290 "Human":"Test", | |
291 "Chimp":"Test", | |
292 "Node12":"Test", | |
293 "Node8":"Test", | |
294 "Node1":"Test", | |
295 "Rat":"Test", | |
296 "Mouse":"Test" | |
297 } | |
298 }, | |
299 "data partitions":{ | |
300 "0":{ | |
301 "name":"relax.filter.default", | |
302 "coverage":[ | |
303 [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] | |
304 ] | |
305 } | |
306 }, | |
307 "branch attributes":{ | |
308 "0":{ | |
309 "Human":{ | |
310 "original name":"Human", | |
311 "Nucleotide GTR":0, | |
312 "MG94xREV with separate rates for branch sets":0, | |
313 "General descriptive":0, | |
314 "k (general descriptive)":0.7168352052656061, | |
315 "RELAX alternative":0, | |
316 "RELAX null":0, | |
317 "RELAX partitioned descriptive":0 | |
318 }, | |
319 "Chimp":{ | |
320 "original name":"Chimp", | |
321 "Nucleotide GTR":0.001818722292071369, | |
322 "MG94xREV with separate rates for branch sets":0.001828056639868651, | |
323 "General descriptive":0.001850581335499795, | |
324 "k (general descriptive)":2.329184252362038, | |
325 "RELAX alternative":0.001831548027528597, | |
326 "RELAX null":0.001835680183060623, | |
327 "RELAX partitioned descriptive":0.00183255534978807 | |
328 }, | |
329 "Baboon":{ | |
330 "original name":"Baboon", | |
331 "Nucleotide GTR":0.001682319705247233, | |
332 "MG94xREV with separate rates for branch sets":0.001770013551346919, | |
333 "General descriptive":0.001869883333754939, | |
334 "k (general descriptive)":0.1228116964827354, | |
335 "RELAX alternative":0.001867314836287998, | |
336 "RELAX null":0.001853697678697539, | |
337 "RELAX partitioned descriptive":0.00189422569191071 | |
338 }, | |
339 "RhMonkey":{ | |
340 "original name":"RhMonkey", | |
341 "Nucleotide GTR":0.003776495523121213, | |
342 "MG94xREV with separate rates for branch sets":0.003720554271464007, | |
343 "General descriptive":0.003663070393385353, | |
344 "k (general descriptive)":2.272939790126477, | |
345 "RELAX alternative":0.003641537789305734, | |
346 "RELAX null":0.003670955010908306, | |
347 "RELAX partitioned descriptive":0.003632158699516803 | |
348 }, | |
349 "Cow":{ | |
350 "original name":"Cow", | |
351 "Nucleotide GTR":0.2483201583381086, | |
352 "MG94xREV with separate rates for branch sets":0.2522875145085426, | |
353 "General descriptive":0.3735091756053704, | |
354 "k (general descriptive)":1.19957642031092, | |
355 "RELAX alternative":0.3407703477665083, | |
356 "RELAX null":0.2958310860090909, | |
357 "RELAX partitioned descriptive":0.3460604457589064 | |
358 }, | |
359 "Pig":{ | |
360 "original name":"Pig", | |
361 "Nucleotide GTR":0.1871417867164377, | |
362 "MG94xREV with separate rates for branch sets":0.1903173961963296, | |
363 "General descriptive":0.2109384940367451, | |
364 "k (general descriptive)":0.6656155688777629, | |
365 "RELAX alternative":0.197167672065417, | |
366 "RELAX null":0.2182629931612711, | |
367 "RELAX partitioned descriptive":0.2076369268997903 | |
368 }, | |
369 "Horse":{ | |
370 "original name":"Horse", | |
371 "Nucleotide GTR":0.2091567334932583, | |
372 "MG94xREV with separate rates for branch sets":0.2159358728261337, | |
373 "General descriptive":0.2810540078141565, | |
374 "k (general descriptive)":0.8115699858212525, | |
375 "RELAX alternative":0.3032889682089364, | |
376 "RELAX null":0.2571098559672552, | |
377 "RELAX partitioned descriptive":0.3026705354406338 | |
378 }, | |
379 "Cat":{ | |
380 "original name":"Cat", | |
381 "Nucleotide GTR":0.2660040109418023, | |
382 "MG94xREV with separate rates for branch sets":0.2795692100037539, | |
383 "General descriptive":0.3635335087937213, | |
384 "k (general descriptive)":0.9728289997736356, | |
385 "RELAX alternative":0.3660889485578829, | |
386 "RELAX null":0.3281803512051322, | |
387 "RELAX partitioned descriptive":0.370631318143086 | |
388 }, | |
389 "Mouse":{ | |
390 "original name":"Mouse", | |
391 "Nucleotide GTR":0.1182531454610134, | |
392 "MG94xREV with separate rates for branch sets":0.1199409901922202, | |
393 "General descriptive":0.1313354563273305, | |
394 "k (general descriptive)":0.2294495132372282, | |
395 "RELAX alternative":0.1341640738853253, | |
396 "RELAX null":0.1483938193994467, | |
397 "RELAX partitioned descriptive":0.1476318125310598 | |
398 }, | |
399 "Rat":{ | |
400 "original name":"Rat", | |
401 "Nucleotide GTR":0.06669544716210057, | |
402 "MG94xREV with separate rates for branch sets":0.06725647453745125, | |
403 "General descriptive":0.07175915155128718, | |
404 "k (general descriptive)":0.5208088414555363, | |
405 "RELAX alternative":0.0724007498013708, | |
406 "RELAX null":0.07365614414375878, | |
407 "RELAX partitioned descriptive":0.07568744563050285 | |
408 }, | |
409 "Node1":{ | |
410 "Nucleotide GTR":0.2771601504028877, | |
411 "MG94xREV with separate rates for branch sets":0.286127507474972, | |
412 "General descriptive":0.3532216661512288, | |
413 "k (general descriptive)":0.2199586786715634, | |
414 "RELAX alternative":0.3833004811985787, | |
415 "RELAX null":0.4576044234710181, | |
416 "RELAX partitioned descriptive":0.4360897576025625 | |
417 }, | |
418 "Node12":{ | |
419 "Nucleotide GTR":0.01783222754921504, | |
420 "MG94xREV with separate rates for branch sets":0.01799298835381691, | |
421 "General descriptive":0.01771170858901891, | |
422 "k (general descriptive)":0.1560499010177516, | |
423 "RELAX alternative":0.01833338832069913, | |
424 "RELAX null":0.01828012634520382, | |
425 "RELAX partitioned descriptive":0.01877701767421286 | |
426 }, | |
427 "Node2":{ | |
428 "Nucleotide GTR":0.06619118337434968, | |
429 "MG94xREV with separate rates for branch sets":0.06192085035608558, | |
430 "General descriptive":0.05843310574046084, | |
431 "k (general descriptive)":0.2816499194095207, | |
432 "RELAX alternative":0.05469841675490748, | |
433 "RELAX null":0.06219694236954142, | |
434 "RELAX partitioned descriptive":0.06011281230238084 | |
435 }, | |
436 "Node3":{ | |
437 "Nucleotide GTR":0.09883746945145887, | |
438 "MG94xREV with separate rates for branch sets":0.09744342239018626, | |
439 "General descriptive":0.1340338084149808, | |
440 "k (general descriptive)":0.8358980179450297, | |
441 "RELAX alternative":0.1164056814082033, | |
442 "RELAX null":0.1282588343299434, | |
443 "RELAX partitioned descriptive":0.1194563668460339 | |
444 }, | |
445 "Node8":{ | |
446 "Nucleotide GTR":0.106110061225871, | |
447 "MG94xREV with separate rates for branch sets":0.1090208137603471, | |
448 "General descriptive":0.1401594332730181, | |
449 "k (general descriptive)":0.9135621448569878, | |
450 "RELAX alternative":0.1275155316795084, | |
451 "RELAX null":0.1346842719904758, | |
452 "RELAX partitioned descriptive":0.1358683972849559 | |
453 }, | |
454 "Node9":{ | |
455 "Nucleotide GTR":0.02567391471029082, | |
456 "MG94xREV with separate rates for branch sets":0.02582385148170195, | |
457 "General descriptive":0.02665352479510937, | |
458 "k (general descriptive)":0.1089752436854629, | |
459 "RELAX alternative":0.02681134359856903, | |
460 "RELAX null":0.02759760291393045, | |
461 "RELAX partitioned descriptive":0.02746061131173372 | |
462 } | |
463 }, | |
464 "attributes":{ | |
465 "original name":{ | |
466 "attribute type":"node label", | |
467 "display order":-1 | |
468 }, | |
469 "Nucleotide GTR":{ | |
470 "attribute type":"branch length", | |
471 "display order":0 | |
472 }, | |
473 "MG94xREV with separate rates for branch sets":{ | |
474 "attribute type":"branch length", | |
475 "display order":1 | |
476 }, | |
477 "General descriptive":{ | |
478 "attribute type":"branch length", | |
479 "display order":4 | |
480 }, | |
481 "k (general descriptive)":{ | |
482 "attribute type":"branch label", | |
483 "display order":4 | |
484 }, | |
485 "RELAX alternative":{ | |
486 "attribute type":"branch length", | |
487 "display order":2 | |
488 }, | |
489 "RELAX null":{ | |
490 "attribute type":"branch length", | |
491 "display order":3 | |
492 }, | |
493 "RELAX partitioned descriptive":{ | |
494 "attribute type":"branch length", | |
495 "display order":5 | |
496 } | |
497 } | |
498 } | |
499 } |