Mercurial > repos > iuc > hyphy_sm19

comparison test-data/busted-out1.json @ 0:ae7c42d49717 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 12:25:55 -0400
parents
children d2acd8d86e55
comparison
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-1:000000000000 0:ae7c42d49717
1 {
2 "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.",
4 "version":"1.2",
5 "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",
8 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
9 },
10 "input":{
11 "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.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 "background":0,
20 "fits":{
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23 "estimated parameters":24,
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31 "Rate Distributions":{
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33 "Substitution rate from nucleotide A to nucleotide G":1,
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35 "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
36 "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
37 "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
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39 "display order":0
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41 "MG94xREV with separate rates for branch sets":{
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188 },
189 "Evidence Ratios":{
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195 ]
196 },
197 "tested":{
198 "0":{
199 "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",
214 "Mouse":"test"
215 }
216 },
217 "data partitions":{
218 "0":{
219 "name":"busted.filter.default",
220 "coverage":[
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]
222 ]
223 }
224 },
225 "branch attributes":{
226 "0":{
227 "Human":{
228 "original name":"Human",
229 "Nucleotide GTR":0,
230 "MG94xREV with separate rates for branch sets":0,
231 "unconstrained":0,
232 "constrained":0
233 },
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 }
361 }