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comparison test-data/absrel-out1.json @ 0:419cd817299c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
author iuc
date Thu, 17 Jan 2019 04:22:13 -0500
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1 {
2 "analysis":{
3 "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.",
4 "version":"2.0",
5 "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",
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"
9 },
10 "input":{
11 "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_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":-3531.96369518556,
22 "estimated parameters":24,
23 "AIC-c":7112.577796875186,
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":0.5474707834424497,
32 "Substitution rate from nucleotide A to nucleotide G":1,
33 "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
34 "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
35 "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
36 "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
37 },
38 "display order":0
39 },
40 "Baseline MG94xREV":{
41 "Log Likelihood":-3450.669934819203,
42 "estimated parameters":46,
43 "AIC-c":6995.711784065174,
44 "Equilibrium frequencies":[
45 [0.04787662253946073],
46 [0.03913388100305117],
47 [0.04844580322128512],
48 [0.0407178971288476],
49 [0.01817959331488358],
50 [0.01485982100934833],
51 [0.01839572120297191],
52 [0.01546129971531724],
53 [0.0190238172858878],
54 [0.01554988139098808],
55 [0.01924998172104109],
56 [0.01617929156565557],
57 [0.02798385246472159],
58 [0.02287372613761008],
59 [0.02831653817605838],
60 [0.02379958245776909],
61 [0.01680670574479072],
62 [0.01373763619452979],
63 [0.01700651207463693],
64 [0.01429369239710176],
65 [0.006381800954137531],
66 [0.005216421415661322],
67 [0.006457670922102578],
68 [0.00542756570877943],
69 [0.006678159032689796],
70 [0.005458661598138652],
71 [0.00675755225029668],
72 [0.00567961101013393],
73 [0.009823507779659469],
74 [0.008029638769211124],
75 [0.009940294440024354],
76 [0.008354653231583485],
77 [0.0329096029621651],
78 [0.02689998621179963],
79 [0.03330084840219455],
80 [0.02798881284619018],
81 [0.01249635346589736],
82 [0.01021439657952951],
83 [0.01264491622176376],
84 [0.01062784315018763],
85 [0.01307665913959002],
86 [0.01068873273724336],
87 [0.0132321208528494],
88 [0.01112137894012831],
89 [0.01923563996618058],
90 [0.01572302316926395],
91 [0.01946432265285621],
92 [0.01635944157725275],
93 [0.01977100255021048],
94 [0.02057127040149398],
95 [0.009184593415672956],
96 [0.007507396443725858],
97 [0.009293784349897772],
98 [0.007811272183233558],
99 [0.007856024926654371],
100 [0.009725369116048951],
101 [0.008174012048031599],
102 [0.01413784690564137],
103 [0.01155613719386138],
104 [0.01430592453757226],
105 [0.01202389319448819]
106 ],
107 "Rate Distributions":{
108 "Per-branch omega":{
109 "Mean":666666667.6064719,
110 "Median":1.103169534345197,
111 "2.5%":0,
112 "97.5%":10000000000
113 }
114 },
115 "display order":1
116 },
117 "Full adaptive model":{
118 "Log Likelihood":-3414.992415597899,
119 "estimated parameters":60,
120 "AIC-c":6954.031265689993,
121 "Rate Distributions":{
122 },
123 "display order":2
124 }
125 },
126 "timers":{
127 "Overall":{
128 "timer":98,
129 "order":0
130 },
131 "Preliminary model fitting":{
132 "timer":0,
133 "order":1
134 },
135 "Baseline model fitting":{
136 "timer":1,
137 "order":2
138 },
139 "Complexity analysis":{
140 "timer":36,
141 "order":3
142 },
143 "Full adaptive model fitting":{
144 "timer":8,
145 "order":4
146 },
147 "Testing for selection":{
148 "timer":53,
149 "order":5
150 }
151 },
152 "test results":{
153 "P-value threshold":0.05,
154 "tested":16,
155 "positive test results":3
156 },
157 "tested":{
158 "0":{
159 "Pig":"test",
160 "Cow":"test",
161 "Node3":"test",
162 "Horse":"test",
163 "Cat":"test",
164 "Node2":"test",
165 "RhMonkey":"test",
166 "Baboon":"test",
167 "Node9":"test",
168 "Human":"test",
169 "Chimp":"test",
170 "Node12":"test",
171 "Node8":"test",
172 "Node1":"test",
173 "Rat":"test",
174 "Mouse":"test"
175 }
176 },
177 "data partitions":{
178 "0":{
179 "name":"absrel.filter.default",
180 "coverage":[
181 [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]
182 ]
183 }
184 },
185 "branch attributes":{
186 "0":{
187 "Human":{
188 "original name":"Human",
189 "Nucleotide GTR":0,
190 "Baseline MG94xREV":0,
191 "Baseline MG94xREV omega ratio":1,
192 "Rate classes":1,
193 "Full adaptive model":0,
194 "Rate Distributions":[
195 [1, 1]
196 ],
197 "LRT":0,
198 "Uncorrected P-value":1,
199 "Corrected P-value":1
200 },
201 "Chimp":{
202 "original name":"Chimp",
203 "Nucleotide GTR":0.001818174796225333,
204 "Baseline MG94xREV":0.001839770270131542,
205 "Baseline MG94xREV omega ratio":10000000000,
206 "Rate classes":1,
207 "Full adaptive model":0.001845806111200226,
208 "Rate Distributions":[
209 [10000000000, 1]
210 ],
211 "LRT":0.6362875427803374,
212 "Uncorrected P-value":0.303261123771571,
213 "Corrected P-value":1
214 },
215 "Baboon":{
216 "original name":"Baboon",
217 "Nucleotide GTR":0.001682034724848474,
218 "Baseline MG94xREV":0.001821072110941238,
219 "Baseline MG94xREV omega ratio":0,
220 "Rate classes":1,
221 "Full adaptive model":0.001808294153407354,
222 "Rate Distributions":[
223 [0, 1]
224 ],
225 "LRT":0,
226 "Uncorrected P-value":1,
227 "Corrected P-value":1
228 },
229 "RhMonkey":{
230 "original name":"RhMonkey",
231 "Nucleotide GTR":0.003775509884015639,
232 "Baseline MG94xREV":0.003671340584166445,
233 "Baseline MG94xREV omega ratio":10000000000,
234 "Rate classes":1,
235 "Full adaptive model":0.003682180830540259,
236 "Rate Distributions":[
237 [10000000000, 1]
238 ],
239 "LRT":1.200615147074132,
240 "Uncorrected P-value":0.2192326116145807,
241 "Corrected P-value":1
242 },
243 "Cow":{
244 "original name":"Cow",
245 "Nucleotide GTR":0.248257545271419,
246 "Baseline MG94xREV":0.2535517510207829,
247 "Baseline MG94xREV omega ratio":1.957039676836281,
248 "Rate classes":2,
249 "Full adaptive model":0.3959632497370367,
250 "Rate Distributions":[
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252 [10.58123012791267, 0.4615587590257811]
253 ],
254 "LRT":24.50128746473001,
255 "Uncorrected P-value":1.583131814197891e-06,
256 "Corrected P-value":2.533010902716626e-05
257 },
258 "Pig":{
259 "original name":"Pig",
260 "Nucleotide GTR":0.1872143003439852,
261 "Baseline MG94xREV":0.1913752025483544,
262 "Baseline MG94xREV omega ratio":1.354835319497051,
263 "Rate classes":1,
264 "Full adaptive model":0.1823079562415392,
265 "Rate Distributions":[
266 [1.270031670375847, 1]
267 ],
268 "LRT":0.5083013304356427,
269 "Uncorrected P-value":0.3278475069550038,
270 "Corrected P-value":1
271 },
272 "Horse":{
273 "original name":"Horse",
274 "Nucleotide GTR":0.2092211101976542,
275 "Baseline MG94xREV":0.2093433205074538,
276 "Baseline MG94xREV omega ratio":1.262933703792719,
277 "Rate classes":2,
278 "Full adaptive model":0.2696870893488891,
279 "Rate Distributions":[
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281 [4.447670371762946, 0.4505673508546879]
282 ],
283 "LRT":9.839972152766677,
284 "Uncorrected P-value":0.002531289908698275,
285 "Corrected P-value":0.03543805872177586
286 },
287 "Cat":{
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289 "Nucleotide GTR":0.2662269345134692,
290 "Baseline MG94xREV":0.2773733494290757,
291 "Baseline MG94xREV omega ratio":1.619113019542315,
292 "Rate classes":2,
293 "Full adaptive model":0.3637840333790108,
294 "Rate Distributions":[
295 [0.3427137549260186, 0.5775012741005606],
296 [6.025097508634321, 0.4224987258994394]
297 ],
298 "LRT":13.05292728184577,
299 "Uncorrected P-value":0.000499814517576469,
300 "Corrected P-value":0.007497217763647035
301 },
302 "Mouse":{
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304 "Nucleotide GTR":0.1181551390736968,
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308 "Full adaptive model":0.1200052061883895,
309 "Rate Distributions":[
310 [0.5418818043457002, 1]
311 ],
312 "LRT":0,
313 "Uncorrected P-value":1,
314 "Corrected P-value":1
315 },
316 "Rat":{
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318 "Nucleotide GTR":0.06673994656462794,
319 "Baseline MG94xREV":0.06546903135094065,
320 "Baseline MG94xREV omega ratio":1.103169534345197,
321 "Rate classes":1,
322 "Full adaptive model":0.06894368446818594,
323 "Rate Distributions":[
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325 ],
326 "LRT":0.04180897168953379,
327 "Uncorrected P-value":0.4613906175252571,
328 "Corrected P-value":1
329 },
330 "Node1":{
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332 "Baseline MG94xREV":0.2903229694372956,
333 "Baseline MG94xREV omega ratio":0.4389914526526448,
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335 "Full adaptive model":0.3664538683295676,
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339 ],
340 "LRT":1.095302853601424,
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342 "Corrected P-value":1
343 },
344 "Node12":{
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349 "Full adaptive model":0.01648897148329989,
350 "Rate Distributions":[
351 [0.3341484726344874, 1]
352 ],
353 "LRT":0,
354 "Uncorrected P-value":1,
355 "Corrected P-value":1
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357 "Node2":{
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368 "Uncorrected P-value":0.007599562698001494,
369 "Corrected P-value":0.09119475237601793
370 },
371 "Node3":{
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377 "Rate Distributions":[
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381 "LRT":6.598417720076213,
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383 "Corrected P-value":0.1442660592625483
384 },
385 "Node8":{
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393 [33.32075865076668, 0.09221592948609958]
394 ],
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397 "Corrected P-value":0.08475169004356781
398 },
399 "Node9":{
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405 "Rate Distributions":[
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408 "LRT":0,
409 "Uncorrected P-value":1,
410 "Corrected P-value":1
411 }
412 },
413 "attributes":{
414 "original name":{
415 "attribute type":"node label",
416 "display order":-1
417 },
418 "Nucleotide GTR":{
419 "attribute type":"branch length",
420 "display order":0
421 },
422 "Baseline MG94xREV":{
423 "attribute type":"branch length",
424 "display order":1
425 },
426 "Baseline MG94xREV omega ratio":{
427 "attribute type":"branch label",
428 "display order":1
429 },
430 "Rate classes":{
431 "attribute type":"branch label",
432 "display order":2
433 },
434 "Full adaptive model":{
435 "attribute type":"branch length",
436 "display order":2
437 },
438 "Rate Distributions":{
439 "attribute type":"branch label",
440 "display order":3
441 },
442 "LRT":{
443 "attribute type":"branch label",
444 "display order":4
445 },
446 "Uncorrected P-value":{
447 "attribute type":"branch label",
448 "display order":5
449 },
450 "Corrected P-value":{
451 "attribute type":"branch label",
452 "display order":6
453 }
454 }
455 }
456 }