Mercurial > repos > iuc > hyphy_fubar

comparison test-data/busted-out2-1.json @ 26:cd41e7a4d35f 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 18:04:56 +0000
parents
children 90e57f65ddd9
comparison
equal deleted inserted replaced
25:296409764676 26:cd41e7a4d35f
1 {
2 "Evidence Ratios":{
3 "constrained": [
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19 ]
20 },
21 "analysis":{
22 "authors":"Sergei L Kosakovsky Pond",
23 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
24 "contact":"spond@temple.edu",
25 "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",
26 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
27 "version":"3.1"
28 },
29 "background":0,
30 "branch attributes":{
31 "0":{
32 "B_FR_83_HXB2":{
33 "MG94xREV with separate rates for branch sets":0.01243274064118979,
34 "Nucleotide GTR":0.01178680392701259,
35 "constrained":0.01256398347964253,
36 "original name":"B_FR_83_HXB2",
37 "unconstrained":0.01346367617740634
38 },
39 "B_US_83_RF":{
40 "MG94xREV with separate rates for branch sets":0.02861520854418918,
41 "Nucleotide GTR":0.02637179869727959,
42 "constrained":0.02907713203932123,
43 "original name":"B_US_83_RF",
44 "unconstrained":0.03296423032791345
45 },
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47 "MG94xREV with separate rates for branch sets":0.01913497611653954,
48 "Nucleotide GTR":0.01766254318226218,
49 "constrained":0.01932498128977916,
50 "original name":"B_US_86_JRFL",
51 "unconstrained":0.02067264364489925
52 },
53 "B_US_90_WEAU160":{
54 "MG94xREV with separate rates for branch sets":0.02258152057123029,
55 "Nucleotide GTR":0.0208836028381146,
56 "constrained":0.02318748492797678,
57 "original name":"B_US_90_WEAU160",
58 "unconstrained":0.02519768979779986
59 },
60 "D_CD_83_ELI":{
61 "MG94xREV with separate rates for branch sets":0.02096470337130958,
62 "Nucleotide GTR":0.01905599613120992,
63 "constrained":0.02057807476219352,
64 "original name":"D_CD_83_ELI",
65 "unconstrained":0.02169258688744172
66 },
67 "D_CD_83_NDK":{
68 "MG94xREV with separate rates for branch sets":0.01034012674036274,
69 "Nucleotide GTR":0.009776698714183414,
70 "constrained":0.0105101167818647,
71 "original name":"D_CD_83_NDK",
72 "unconstrained":0.01040169158313715
73 },
74 "D_CD_84_84ZR085":{
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76 "Nucleotide GTR":0.02822254903672137,
77 "constrained":0.03140845141419388,
78 "original name":"D_CD_84_84ZR085",
79 "unconstrained":0.03388014669054998
80 },
81 "D_UG_94_94UG114":{
82 "MG94xREV with separate rates for branch sets":0.0597102708893009,
83 "Nucleotide GTR":0.05323070232023583,
84 "constrained":0.06218362660429492,
85 "original name":"D_UG_94_94UG114",
86 "unconstrained":0.06804948826756697
87 },
88 "Node1":{
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90 "Nucleotide GTR":0.02355240508560319,
91 "constrained":0.02779997592087442,
92 "unconstrained":0.02940126303315396
93 },
94 "Node10":{
95 "MG94xREV with separate rates for branch sets":0.00193736936681532,
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97 "constrained":0.001848018461605612,
98 "unconstrained":0.001859856019153286
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100 "Node2":{
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102 "Nucleotide GTR":0.003949360371801276,
103 "constrained":0.00346172246250584,
104 "unconstrained":0.002261770932022259
105 },
106 "Node3":{
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110 "unconstrained":0.01401270546560647
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114 "Nucleotide GTR":0.004986123424162501,
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116 "unconstrained":0.005520113121560347
117 }
118 },
119 "attributes":{
120 "MG94xREV with separate rates for branch sets":{
121 "attribute type":"branch length",
122 "display order":1
123 },
124 "Nucleotide GTR":{
125 "attribute type":"branch length",
126 "display order":0
127 },
128 "constrained":{
129 "attribute type":"branch length",
130 "display order":1
131 },
132 "original name":{
133 "attribute type":"node label",
134 "display order":0
135 },
136 "unconstrained":{
137 "attribute type":"branch length",
138 "display order":0
139 }
140 }
141 },
142 "data partitions":{
143 "0":{
144 "coverage": [
145 [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, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439]
146 ],
147 "name":"busted.filter.default"
148 }
149 },
150 "fits":{
151 "Constrained model":{
152 "AIC-c":6398.612664722735,
153 "Log Likelihood":-3168.021928691643,
154 "Rate Distributions":{
155 "Test":{
156 "0":{
157 "omega":0,
158 "proportion":0.6914129319908371
159 },
160 "1":{
161 "omega":0,
162 "proportion":0.07568144722655729
163 },
164 "2":{
165 "omega":1,
166 "proportion":0.2329056207826056
167 }
168 }
169 },
170 "display order":3,
171 "estimated parameters":31
172 },
173 "MG94xREV with separate rates for branch sets":{
174 "AIC-c":6408.899382280021,
175 "Equilibrium frequencies": [
176 [0.07535940345366139],
177 [0.01443006409728228],
178 [0.02915821068672351],
179 [0.02954870567752823],
180 [0.03219408024958758],
181 [0.006164627375802654],
182 [0.01245659774045292],
183 [0.01262342001471309],
184 [0.0276793164843978],
185 [0.005300125700761717],
186 [0.01070973633984303],
187 [0.01085316415297191],
188 [0.0418125103783387],
189 [0.008006395714089126],
190 [0.01617817990958604],
191 [0.0163948426631036],
192 [0.0409913146415633],
193 [0.007849150478922548],
194 [0.01586044121725868],
195 [0.01607284872448998],
196 [0.01751178502783737],
197 [0.003353213651232053],
198 [0.006775694789785172],
199 [0.006866436807635995],
200 [0.01505600521072376],
201 [0.002882972930821469],
202 [0.005825499564956559],
203 [0.005903516300053625],
204 [0.02274367484777162],
205 [0.004355032959661065],
206 [0.008800028033786655],
207 [0.008917880494044083],
208 [0.06143704799998004],
209 [0.01176416611541591],
210 [0.0237713451467977],
211 [0.0240896977132239],
212 [0.0262463496652457],
213 [0.005025736545566795],
214 [0.01015528996016046],
215 [0.01029129247081581],
216 [0.02256567087217255],
217 [0.004320948178469224],
218 [0.008731154380523415],
219 [0.00884808446536876],
220 [0.034087812394816],
221 [0.006527245376826684],
222 [0.01318932435908579],
223 [0.01336595951511979],
224 [0.01178447449308153],
225 [0.02413128354890585],
226 [0.0262916585104385],
227 [0.005034412430862358],
228 [0.01017282094890981],
229 [0.01030905823951665],
230 [0.004328407393735399],
231 [0.008746226896405704],
232 [0.008863358836639712],
233 [0.03414665788893068],
234 [0.006538513303760755],
235 [0.0132120929750345],
236 [0.01338903305480236]
237 ],
238 "Log Likelihood":-3176.217093030587,
239 "Rate Distributions":{
240 "non-synonymous/synonymous rate ratio for *test*": [
241 [0.231720664913378, 1]
242 ]
243 },
244 "display order":1,
245 "estimated parameters":28
246 },
247 "Nucleotide GTR":{
248 "AIC-c":6683.094244259512,
249 "Equilibrium frequencies": [
250 [0.4044507575757576],
251 [0.1662878787878788],
252 [0.2095643939393939],
253 [0.2196969696969697]
254 ],
255 "Log Likelihood":-3320.503280793639,
256 "Rate Distributions":{
257 "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,
258 "Substitution rate from nucleotide A to nucleotide G":1,
259 "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,
260 "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,
261 "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,
262 "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568
263 },
264 "display order":0,
265 "estimated parameters":21
266 },
267 "Unconstrained model":{
268 "AIC-c":6391.938375474656,
269 "Log Likelihood":-3163.666348620609,
270 "Rate Distributions":{
271 "Test":{
272 "0":{
273 "omega":0.1490485393860332,
274 "proportion":0.02658974082564446
275 },
276 "1":{
277 "omega":0.169565784922581,
278 "proportion":0.9641001770967245
279 },
280 "2":{
281 "omega":15.09387961636913,
282 "proportion":0.009310082077631076
283 }
284 }
285 },
286 "display order":2,
287 "estimated parameters":32
288 }
289 },
290 "input":{
291 "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex",
292 "number of sequences":8,
293 "number of sites":440,
294 "partition count":1,
295 "trees":{
296 "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"
297 }
298 },
299 "test results":{
300 "LRT":8.711160142067456,
301 "p-value":0.006417496108925114
302 },
303 "tested":{
304 "0":{
305 "B_FR_83_HXB2":"test",
306 "B_US_83_RF":"test",
307 "B_US_86_JRFL":"test",
308 "B_US_90_WEAU160":"test",
309 "D_CD_83_ELI":"test",
310 "D_CD_83_NDK":"test",
311 "D_CD_84_84ZR085":"test",
312 "D_UG_94_94UG114":"test",
313 "Node1":"test",
314 "Node10":"test",
315 "Node2":"test",
316 "Node3":"test",
317 "Node9":"test"
318 }
319 },
320 "timers":{
321 "Constrained BUSTED model fitting":{
322 "order":3,
323 "timer":23
324 },
325 "Overall":{
326 "order":0,
327 "timer":133
328 },
329 "Preliminary model fitting":{
330 "order":1,
331 "timer":4
332 },
333 "Unconstrained BUSTED model fitting":{
334 "order":2,
335 "timer":105
336 }
337 }
338 }