Mercurial > repos > iuc > hyphy_relax

comparison test-data/busted-out1.json @ 25:a4c5dc437558 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 18:03:51 +0000
parents 1da578d6a253
children
comparison
equal deleted inserted replaced
24:098451b762fb 25:a4c5dc437558
1 { 1 {
2 "Evidence Ratios":{ 2 "Evidence Ratios":{
3 "constrained": [ 3 "constrained": [
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9 }, 9 },
10 "Site Log Likelihood":{ 10 "Site Log Likelihood":{
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25 ], 25 ],
26 "analysis":{ 26 "analysis":{
27 "authors":"Sergei L Kosakovsky Pond", 27 "authors":"Sergei L Kosakovsky Pond",
28 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71", 28 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
29 "contact":"spond@temple.edu", 29 "contact":"spond@temple.edu",
30 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n", 30 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", 31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
32 "version":"3.0" 32 "version":"3.1"
33 }, 33 },
34 "background":0, 34 "background":0,
35 "branch attributes":{ 35 "branch attributes":{
36 "0":{ 36 "0":{
37 "Baboon":{ 37 "Baboon":{
38 "MG94xREV with separate rates for branch sets":0.001771850913718116, 38 "MG94xREV with separate rates for branch sets":0.001772434847524003,
39 "Nucleotide GTR":0.00167976779100812, 39 "Nucleotide GTR":0.001680040630127455,
40 "constrained":0.0005055252388761481, 40 "constrained":0.001513413708231178,
41 "original name":"Baboon", 41 "original name":"Baboon",
42 "unconstrained":0.0005398732671668005 42 "unconstrained":0.00161713005248515
43 }, 43 },
44 "Cat":{ 44 "Cat":{
45 "MG94xREV with separate rates for branch sets":0.2738959056554072, 45 "MG94xREV with separate rates for branch sets":0.2735065373507703,
46 "Nucleotide GTR":0.266075486389923, 46 "Nucleotide GTR":0.2660909938917123,
47 "constrained":0.1152712488116292, 47 "constrained":0.3466844629529476,
48 "original name":"Cat", 48 "original name":"Cat",
49 "unconstrained":0.120218071527276 49 "unconstrained":0.3607268493024173
50 }, 50 },
51 "Chimp":{ 51 "Chimp":{
52 "MG94xREV with separate rates for branch sets":0.001827968855137289, 52 "MG94xREV with separate rates for branch sets":0.001828401123834132,
53 "Nucleotide GTR":0.001817801565830578, 53 "Nucleotide GTR":0.001818373670119325,
54 "constrained":0.0006181497274348637, 54 "constrained":0.001854421055569225,
55 "original name":"Chimp", 55 "original name":"Chimp",
56 "unconstrained":0.0006183542388399873 56 "unconstrained":0.001853794709397617
57 }, 57 },
58 "Cow":{ 58 "Cow":{
59 "MG94xREV with separate rates for branch sets":0.2477119781238836, 59 "MG94xREV with separate rates for branch sets":0.2477981038577003,
60 "Nucleotide GTR":0.2480176045457076, 60 "Nucleotide GTR":0.2481025999892287,
61 "constrained":0.1036665344622347, 61 "constrained":0.3115800338446564,
62 "original name":"Cow", 62 "original name":"Cow",
63 "unconstrained":0.1088268022245659 63 "unconstrained":0.3266266518611717
64 }, 64 },
65 "Horse":{ 65 "Horse":{
66 "MG94xREV with separate rates for branch sets":0.211203801568566, 66 "MG94xREV with separate rates for branch sets":0.21116782461044,
67 "Nucleotide GTR":0.2090856782081004, 67 "Nucleotide GTR":0.2090310577070883,
68 "constrained":0.08236651201101133, 68 "constrained":0.2473423214593362,
69 "original name":"Horse", 69 "original name":"Horse",
70 "unconstrained":0.08564084427400141 70 "unconstrained":0.2568895651944081
71 }, 71 },
72 "Human":{ 72 "Human":{
73 "MG94xREV with separate rates for branch sets":0, 73 "MG94xREV with separate rates for branch sets":0,
74 "Nucleotide GTR":0, 74 "Nucleotide GTR":0,
75 "constrained":0, 75 "constrained":0,
76 "original name":"Human", 76 "original name":"Human",
77 "unconstrained":0 77 "unconstrained":0
78 }, 78 },
79 "Mouse":{ 79 "Mouse":{
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81 "Nucleotide GTR":0.1181301915748399, 81 "Nucleotide GTR":0.1180171198334285,
82 "constrained":0.04601717170435755, 82 "constrained":0.1381882260320684,
83 "original name":"Mouse", 83 "original name":"Mouse",
84 "unconstrained":0.04942545223877414 84 "unconstrained":0.1482500840848965
85 }, 85 },
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90 "unconstrained":0.1515367890887531 90 "unconstrained":0.4535373691584812
91 }, 91 },
92 "Node12":{ 92 "Node12":{
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95 "constrained":0.005338125135456628, 95 "constrained":0.01603697675468384,
96 "unconstrained":0.00572208893382143 96 "unconstrained":0.01716581823757766
97 }, 97 },
98 "Node2":{ 98 "Node2":{
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100 "Nucleotide GTR":0.06616183769400197, 100 "Nucleotide GTR":0.06613162123865737,
101 "constrained":0.02253286838656328, 101 "constrained":0.06766882319669908,
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103 }, 103 },
104 "Node3":{ 104 "Node3":{
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106 "Nucleotide GTR":0.09890202668045614, 106 "Nucleotide GTR":0.09886326330774685,
107 "constrained":0.04280347934583096, 107 "constrained":0.128627313187861,
108 "unconstrained":0.04618990784049085 108 "unconstrained":0.1385358286963005
109 }, 109 },
110 "Node8":{ 110 "Node8":{
111 "MG94xREV with separate rates for branch sets":0.1096720572321177, 111 "MG94xREV with separate rates for branch sets":0.1095532710088725,
112 "Nucleotide GTR":0.10624077635158, 112 "Nucleotide GTR":0.106239268140425,
113 "constrained":0.04415239867414091, 113 "constrained":0.1326559254556453,
114 "unconstrained":0.04768889036449767 114 "unconstrained":0.1430782720540034
115 }, 115 },
116 "Node9":{ 116 "Node9":{
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119 "constrained":0.00997308939110993, 119 "constrained":0.02991066003065707,
120 "unconstrained":0.009841415288506062 120 "unconstrained":0.02952913741456189
121 }, 121 },
122 "Pig":{ 122 "Pig":{
123 "MG94xREV with separate rates for branch sets":0.1928073761020463, 123 "MG94xREV with separate rates for branch sets":0.1925158663261413,
124 "Nucleotide GTR":0.1871746592118726, 124 "Nucleotide GTR":0.1871893456388788,
125 "constrained":0.07816490289585476, 125 "constrained":0.2351007649069627,
126 "original name":"Pig", 126 "original name":"Pig",
127 "unconstrained":0.08275992348314189 127 "unconstrained":0.248176820169511
128 }, 128 },
129 "Rat":{ 129 "Rat":{
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131 "Nucleotide GTR":0.06656862018951525, 131 "Nucleotide GTR":0.06661283005976348,
132 "constrained":0.02277034233250765, 132 "constrained":0.06832918896283274,
133 "original name":"Rat", 133 "original name":"Rat",
134 "unconstrained":0.02372534359054489 134 "unconstrained":0.07114161288708017
135 }, 135 },
136 "RhMonkey":{ 136 "RhMonkey":{
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138 "Nucleotide GTR":0.003775504255522691, 138 "Nucleotide GTR":0.003775170135617877,
139 "constrained":0.001359450941376631, 139 "constrained":0.004078975866589158,
140 "original name":"RhMonkey", 140 "original name":"RhMonkey",
141 "unconstrained":0.00132482447204072 141 "unconstrained":0.003977618821878279
142 } 142 }
143 }, 143 },
144 "attributes":{ 144 "attributes":{
145 "MG94xREV with separate rates for branch sets":{ 145 "MG94xREV with separate rates for branch sets":{
146 "attribute type":"branch length", 146 "attribute type":"branch length",
172 "name":"busted.filter.default" 172 "name":"busted.filter.default"
173 } 173 }
174 }, 174 },
175 "fits":{ 175 "fits":{
176 "Constrained model":{ 176 "Constrained model":{
177 "AIC-c":6918.851822592964, 177 "AIC-c":6918.865252134614,
178 "Log Likelihood":-3419.573452280089, 178 "Log Likelihood":-3419.580167050914,
179 "Rate Distributions":{ 179 "Rate Distributions":{
180 "Synonymous site-to-site rates":{ 180 "Synonymous site-to-site rates":{
181 "0":{ 181 "0":{
182 "proportion":0.3289898788632067, 182 "proportion":0.3286044813984554,
183 "rate":0.3124849036133048 183 "rate":0.3114745230555425
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189 "2":{ 189 "2":{
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191 "rate":3.115265578623139 191 "rate":3.135858111155513
192 } 192 }
193 }, 193 },
194 "Test":{ 194 "Test":{
195 "0":{ 195 "0":{
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197 "proportion":0.02093092071081848 197 "proportion":0.1610337459523823
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199 "1":{ 199 "1":{
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203 "2":{ 203 "2":{
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205 "proportion":0.8403256984411339 205 "proportion":0.8389662540476177
206 } 206 }
207 } 207 }
208 }, 208 },
209 "display order":3, 209 "display order":3,
210 "estimated parameters":39 210 "estimated parameters":39
211 }, 211 },
212 "MG94xREV with separate rates for branch sets":{ 212 "MG94xREV with separate rates for branch sets":{
213 "AIC-c":6997.089050462658, 213 "AIC-c":6997.104847699299,
214 "Equilibrium frequencies": [ 214 "Equilibrium frequencies": [
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276 ], 276 ],
277 "Log Likelihood":-3467.004808147542, 277 "Log Likelihood":-3467.012706765863,
278 "Rate Distributions":{ 278 "Rate Distributions":{
279 "non-synonymous/synonymous rate ratio for *test*": [ 279 "non-synonymous/synonymous rate ratio for *test*": [
280 [0.9950576192409499, 1] 280 [0.9959842858928788, 1]
281 ] 281 ]
282 }, 282 },
283 "display order":1, 283 "display order":1,
284 "estimated parameters":31 284 "estimated parameters":31
285 }, 285 },
286 "Nucleotide GTR":{ 286 "Nucleotide GTR":{
287 "AIC-c":7112.85745601076, 287 "AIC-c":7112.857310169033,
288 "Equilibrium frequencies": [ 288 "Equilibrium frequencies": [
289 [0.3592490842490842], 289 [0.3592490842490842],
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292 [0.2187728937728937] 292 [0.2187728937728937]
293 ], 293 ],
294 "Log Likelihood":-3532.321297387654, 294 "Log Likelihood":-3532.32122446679,
295 "Rate Distributions":{ 295 "Rate Distributions":{
296 "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497, 296 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
297 "Substitution rate from nucleotide A to nucleotide G":1, 297 "Substitution rate from nucleotide A to nucleotide G":1,
298 "Substitution rate from nucleotide A to nucleotide T":0.264666902964203, 298 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
299 "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098, 299 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
300 "Substitution rate from nucleotide C to nucleotide T":1.027924764411573, 300 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
301 "Substitution rate from nucleotide G to nucleotide T":0.304615404570875 301 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
302 }, 302 },
303 "display order":0, 303 "display order":0,
304 "estimated parameters":24 304 "estimated parameters":24
305 }, 305 },
306 "Unconstrained model":{ 306 "Unconstrained model":{
307 "AIC-c":6910.766610587704, 307 "AIC-c":6910.776988890891,
308 "Log Likelihood":-3414.486640449675, 308 "Log Likelihood":-3414.491829601268,
309 "Rate Distributions":{ 309 "Rate Distributions":{
310 "Synonymous site-to-site rates":{ 310 "Synonymous site-to-site rates":{
311 "0":{ 311 "0":{
312 "proportion":0.2645541257391169, 312 "proportion":0.2655037162058198,
313 "rate":0.2747941124675511 313 "rate":0.2749303122566129
314 }, 314 },
315 "1":{ 315 "1":{
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317 "rate":0.9734675888351726 317 "rate":0.9740711294478059
318 }, 318 },
319 "2":{ 319 "2":{
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321 "rate":3.028333913894314 321 "rate":3.041695877803997
322 } 322 }
323 }, 323 },
324 "Test":{ 324 "Test":{
325 "0":{ 325 "0":{
326 "omega":0, 326 "omega":0,
327 "proportion":0.04809457608200497 327 "proportion":0.386646389823596
328 }, 328 },
329 "1":{ 329 "1":{
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331 "proportion":0.3410012743721951 331 "proportion":0
332 }, 332 },
333 "2":{ 333 "2":{
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335 "proportion":0.6109041495458 335 "proportion":0.613353610176404
336 } 336 }
337 } 337 }
338 }, 338 },
339 "display order":2, 339 "display order":2,
340 "estimated parameters":40 340 "estimated parameters":40
341 } 341 }
342 }, 342 },
343 "input":{ 343 "input":{
344 "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa", 344 "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta",
345 "number of sequences":10, 345 "number of sequences":10,
346 "number of sites":187, 346 "number of sites":187,
347 "partition count":1, 347 "partition count":1,
348 "trees":{ 348 "trees":{
349 "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)" 349 "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)"
350 } 350 }
351 }, 351 },
352 "test results":{ 352 "test results":{
353 "LRT":10.17362366082671, 353 "LRT":10.17667489929045,
354 "p-value":0.003088842014430382 354 "p-value":0.003084133210483175
355 }, 355 },
356 "tested":{ 356 "tested":{
357 "0":{ 357 "0":{
358 "Baboon":"test", 358 "Baboon":"test",
359 "Cat":"test", 359 "Cat":"test",
374 } 374 }
375 }, 375 },
376 "timers":{ 376 "timers":{
377 "Constrained BUSTED model fitting":{ 377 "Constrained BUSTED model fitting":{
378 "order":3, 378 "order":3,
379 "timer":62 379 "timer":70
380 }, 380 },
381 "Overall":{ 381 "Overall":{
382 "order":0, 382 "order":0,
383 "timer":228 383 "timer":451
384 }, 384 },
385 "Preliminary model fitting":{ 385 "Preliminary model fitting":{
386 "order":1, 386 "order":1,
387 "timer":3 387 "timer":10
388 }, 388 },
389 "Unconstrained BUSTED model fitting":{ 389 "Unconstrained BUSTED model fitting":{
390 "order":2, 390 "order":2,
391 "timer":161 391 "timer":370
392 } 392 }
393 } 393 }
394 } 394 }