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comparison test-data/relax-out1.json @ 1:6c3ece5fb602 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:27:42 -0400
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children 8276bb2adea5
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0:24a2bf70dbdd 1:6c3ece5fb602
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 }