Mercurial > repos > iuc > hyphy_fel
comparison test-data/busted-out1.json @ 2:a8b34daec0d9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author | iuc |
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date | Thu, 13 Feb 2020 15:04:13 -0500 |
parents | 24a2bf70dbdd |
children | 8276bb2adea5 |
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1:6c3ece5fb602 | 2:a8b34daec0d9 |
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1 { | 1 { |
2 "Evidence Ratios":{ | |
3 "constrained": [ | |
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5 ], | |
6 "optimized null": [ | |
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8 ] | |
9 }, | |
10 "Site Log Likelihood":{ | |
11 "constrained": [ | |
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13 ], | |
14 "optimized null": [ | |
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17 "unconstrained": [ | |
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20 }, | |
21 "Synonymous site-posteriors": [ | |
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25 ], | |
2 "analysis":{ | 26 "analysis":{ |
3 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.", | 27 "authors":"Sergei L Kosakovsky Pond", |
4 "version":"1.2", | |
5 "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", |
6 "authors":"Sergei L Kosakovsky Pond", | |
7 "contact":"spond@temple.edu", | 29 "contact":"spond@temple.edu", |
8 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})" | 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", |
31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", | |
32 "version":"3.0" | |
33 }, | |
34 "background":0, | |
35 "branch attributes":{ | |
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37 "Baboon":{ | |
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182 "constrained":[ | |
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184 ], | |
185 "optimized null":[ | |
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187 ] | |
188 }, | |
189 "Evidence Ratios":{ | |
190 "constrained":[ | |
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192 ], | |
193 "optimized null":[ | |
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195 ] | |
196 }, | 355 }, |
197 "tested":{ | 356 "tested":{ |
198 "0":{ | 357 "0":{ |
358 "Baboon":"test", | |
359 "Cat":"test", | |
360 "Chimp":"test", | |
361 "Cow":"test", | |
362 "Horse":"test", | |
363 "Human":"test", | |
364 "Mouse":"test", | |
365 "Node1":"test", | |
366 "Node12":"test", | |
367 "Node2":"test", | |
368 "Node3":"test", | |
369 "Node8":"test", | |
370 "Node9":"test", | |
199 "Pig":"test", | 371 "Pig":"test", |
200 "Cow":"test", | |
201 "Node3":"test", | |
202 "Horse":"test", | |
203 "Cat":"test", | |
204 "Node2":"test", | |
205 "RhMonkey":"test", | |
206 "Baboon":"test", | |
207 "Node9":"test", | |
208 "Human":"test", | |
209 "Chimp":"test", | |
210 "Node12":"test", | |
211 "Node8":"test", | |
212 "Node1":"test", | |
213 "Rat":"test", | 372 "Rat":"test", |
214 "Mouse":"test" | 373 "RhMonkey":"test" |
215 } | 374 } |
216 }, | 375 }, |
217 "data partitions":{ | 376 "timers":{ |
218 "0":{ | 377 "Constrained BUSTED model fitting":{ |
219 "name":"busted.filter.default", | 378 "order":3, |
220 "coverage":[ | 379 "timer":62 |
221 [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] | 380 }, |
222 ] | 381 "Overall":{ |
223 } | 382 "order":0, |
224 }, | 383 "timer":228 |
225 "branch attributes":{ | 384 }, |
226 "0":{ | 385 "Preliminary model fitting":{ |
227 "Human":{ | 386 "order":1, |
228 "original name":"Human", | 387 "timer":3 |
229 "Nucleotide GTR":0, | 388 }, |
230 "MG94xREV with separate rates for branch sets":0, | 389 "Unconstrained BUSTED model fitting":{ |
231 "unconstrained":0, | 390 "order":2, |
232 "constrained":0 | 391 "timer":161 |
233 }, | 392 } |
234 "Chimp":{ | |
235 "original name":"Chimp", | |
236 "Nucleotide GTR":0.001818647577470898, | |
237 "MG94xREV with separate rates for branch sets":0.001828142895085465, | |
238 "unconstrained":0.001835079043904073, | |
239 "constrained":0.001827227299324197 | |
240 }, | |
241 "Baboon":{ | |
242 "original name":"Baboon", | |
243 "Nucleotide GTR":0.001683434956773037, | |
244 "MG94xREV with separate rates for branch sets":0.001771624553208579, | |
245 "unconstrained":0.001852571561323465, | |
246 "constrained":0.001757260248005238 | |
247 }, | |
248 "RhMonkey":{ | |
249 "original name":"RhMonkey", | |
250 "Nucleotide GTR":0.003773669075849421, | |
251 "MG94xREV with separate rates for branch sets":0.003717699096857038, | |
252 "unconstrained":0.003672835047422234, | |
253 "constrained":0.00373144096412681 | |
254 }, | |
255 "Cow":{ | |
256 "original name":"Cow", | |
257 "Nucleotide GTR":0.2483322373763571, | |
258 "MG94xREV with separate rates for branch sets":0.2480141631033857, | |
259 "unconstrained":0.2960120156157274, | |
260 "constrained":0.2592686681333873 | |
261 }, | |
262 "Pig":{ | |
263 "original name":"Pig", | |
264 "Nucleotide GTR":0.187244836750842, | |
265 "MG94xREV with separate rates for branch sets":0.1926081878751187, | |
266 "unconstrained":0.2187526946336905, | |
267 "constrained":0.1943776301130502 | |
268 }, | |
269 "Horse":{ | |
270 "original name":"Horse", | |
271 "Nucleotide GTR":0.2091766851769093, | |
272 "MG94xREV with separate rates for branch sets":0.2111575880588217, | |
273 "unconstrained":0.2572135566477119, | |
274 "constrained":0.218486450878766 | |
275 }, | |
276 "Cat":{ | |
277 "original name":"Cat", | |
278 "Nucleotide GTR":0.266381043956941, | |
279 "MG94xREV with separate rates for branch sets":0.273601177885004, | |
280 "unconstrained":0.3292215104251173, | |
281 "constrained":0.28483085314287 | |
282 }, | |
283 "Mouse":{ | |
284 "original name":"Mouse", | |
285 "Nucleotide GTR":0.1181831744338598, | |
286 "MG94xREV with separate rates for branch sets":0.1201847378516324, | |
287 "unconstrained":0.1489713993010398, | |
288 "constrained":0.1233480139851019 | |
289 }, | |
290 "Rat":{ | |
291 "original name":"Rat", | |
292 "Nucleotide GTR":0.06669700444436912, | |
293 "MG94xREV with separate rates for branch sets":0.0670850471739789, | |
294 "unconstrained":0.07366345007817726, | |
295 "constrained":0.06713082546371778 | |
296 }, | |
297 "Node1":{ | |
298 "Nucleotide GTR":0.276880831396131, | |
299 "MG94xREV with separate rates for branch sets":0.2843521449765504, | |
300 "unconstrained":0.459085769955035, | |
301 "constrained":0.3115534692518958 | |
302 }, | |
303 "Node12":{ | |
304 "Nucleotide GTR":0.01783434870161725, | |
305 "MG94xREV with separate rates for branch sets":0.01788794906051452, | |
306 "unconstrained":0.01828498503175797, | |
307 "constrained":0.01770410398930177 | |
308 }, | |
309 "Node2":{ | |
310 "Nucleotide GTR":0.06617535490721377, | |
311 "MG94xREV with separate rates for branch sets":0.06447679597474805, | |
312 "unconstrained":0.0623969317369398, | |
313 "constrained":0.06097949807503514 | |
314 }, | |
315 "Node3":{ | |
316 "Nucleotide GTR":0.09884524766349881, | |
317 "MG94xREV with separate rates for branch sets":0.1017497956116402, | |
318 "unconstrained":0.1285021744856729, | |
319 "constrained":0.1065011238088613 | |
320 }, | |
321 "Node8":{ | |
322 "Nucleotide GTR":0.1061610073141143, | |
323 "MG94xREV with separate rates for branch sets":0.1093806684969149, | |
324 "unconstrained":0.1348034716617685, | |
325 "constrained":0.1118205234697939 | |
326 }, | |
327 "Node9":{ | |
328 "Nucleotide GTR":0.02568007351415409, | |
329 "MG94xREV with separate rates for branch sets":0.02593963430985144, | |
330 "unconstrained":0.02761127562964508, | |
331 "constrained":0.02639493109700932 | |
332 } | |
333 }, | |
334 "attributes":{ | |
335 "original name":{ | |
336 "attribute type":"node label", | |
337 "display order":0 | |
338 }, | |
339 "Nucleotide GTR":{ | |
340 "attribute type":"branch length", | |
341 "display order":0 | |
342 }, | |
343 "MG94xREV with separate rates for branch sets":{ | |
344 "attribute type":"branch length", | |
345 "display order":1 | |
346 }, | |
347 "unconstrained":{ | |
348 "attribute type":"branch length", | |
349 "display order":0 | |
350 }, | |
351 "constrained":{ | |
352 "attribute type":"branch length", | |
353 "display order":1 | |
354 } | |
355 } | |
356 }, | |
357 "test results":{ | |
358 "LRT":44.77492170961614, | |
359 "p-value":1.893429857346973e-10 | |
360 } | 393 } |
361 } | 394 } |