Mercurial > repos > iuc > hyphy_sm19
view test-data/meme-out1.json @ 10:188452adcaa0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e86817831c8ab0d0f8f86e32c25027cc370947c5"
| author | iuc |
|---|---|
| date | Mon, 27 Apr 2020 12:59:43 -0400 |
| parents | 5f1830cb9135 |
| children |
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at a site for the positive/neutral evolution component"], ["p<sup>+</sup>", "Mixture distribution weight allocated to β<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"], ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β<sup>+</sup> rate"], ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] ] }, "analysis":{ "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", "contact":"spond@temple.edu", "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", "requirements":"in-frame codon alignment and a phylogenetic tree", "version":"2.1.1" }, "branch attributes":{ "0":{ "CHICKEN_CK_160_2005":{ "EBF site 100 (partition 1)":1, "EBF site 102 (partition 1)":0.4618577742407079, "EBF site 104 (partition 1)":1, "EBF site 11 (partition 1)":1, "EBF site 112 (partition 1)":1, "EBF site 113 (partition 1)":1, "EBF site 117 (partition 1)":1, "EBF site 12 (partition 1)":1, "EBF site 136 (partition 1)":1, "EBF site 140 (partition 1)":1, "EBF site 142 (partition 1)":1, "EBF site 145 (partition 1)":1, "EBF site 146 (partition 1)":1, "EBF site 152 (partition 1)":1, "EBF site 153 (partition 1)":1, "EBF site 154 (partition 1)":1, "EBF site 155 (partition 1)":1, "EBF site 156 (partition 1)":1, "EBF site 157 (partition 1)":1, "EBF site 16 (partition 1)":0.8956232595692452, "EBF site 167 (partition 1)":0.2934693500080898, "EBF site 170 (partition 1)":1, "EBF 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(partition 1)":1, "EBF site 506 (partition 1)":0.6145034828797277, "EBF site 509 (partition 1)":1, "EBF site 515 (partition 1)":0.1518467497901648, "EBF site 52 (partition 1)":1, "EBF site 527 (partition 1)":1, "EBF site 529 (partition 1)":1, "EBF site 537 (partition 1)":1, "EBF site 539 (partition 1)":1, "EBF site 545 (partition 1)":1, "EBF site 549 (partition 1)":1, "EBF site 553 (partition 1)":1, "EBF site 558 (partition 1)":76.04690286345168, "EBF site 560 (partition 1)":1, "EBF site 564 (partition 1)":1, "EBF site 58 (partition 1)":1, "EBF site 59 (partition 1)":1, "EBF site 60 (partition 1)":1, "EBF site 68 (partition 1)":1, "EBF site 69 (partition 1)":1, "EBF site 78 (partition 1)":1, "EBF site 79 (partition 1)":1, "EBF site 8 (partition 1)":1, "EBF site 84 (partition 1)":1, "EBF site 86 (partition 1)":1, "EBF site 89 (partition 1)":1, "Global MG94xREV":0.00645863855906697, "Nucleotide GTR":0.006373291987009584, "original name":"CHICKEN_CK_160_2005" }, "CHICKEN_HEBEI_326_2005":{ 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1)":0.5589771102055697, "EBF site 509 (partition 1)":1, "EBF site 515 (partition 1)":0.1243159242286358, "EBF site 52 (partition 1)":1, "EBF site 527 (partition 1)":1, "EBF site 529 (partition 1)":1, "EBF site 537 (partition 1)":1, "EBF site 539 (partition 1)":1, "EBF site 545 (partition 1)":1, "EBF site 549 (partition 1)":1, "EBF site 553 (partition 1)":1, "EBF site 558 (partition 1)":0.6961922557341373, "EBF site 560 (partition 1)":1, "EBF site 564 (partition 1)":1, "EBF site 58 (partition 1)":1, "EBF site 59 (partition 1)":1, "EBF site 60 (partition 1)":1, "EBF site 68 (partition 1)":1, "EBF site 69 (partition 1)":1, "EBF site 78 (partition 1)":1, "EBF site 79 (partition 1)":1, "EBF site 8 (partition 1)":1, "EBF site 84 (partition 1)":1, "EBF site 86 (partition 1)":1, "EBF site 89 (partition 1)":1, "Global MG94xREV":0.007944352318354534, "Nucleotide GTR":0.00775874788653539, "original name":"SWINE_ANHUI_1_2004" } }, "attributes":{ "EBF site 100 (partition 1)":{ "attribute type":"branch label", "display order":102 }, "EBF site 102 (partition 1)":{ "attribute type":"branch label", "display order":104 }, "EBF site 104 (partition 1)":{ "attribute type":"branch label", "display order":106 }, "EBF site 11 (partition 1)":{ "attribute type":"branch label", "display order":13 }, "EBF site 112 (partition 1)":{ "attribute type":"branch label", "display order":114 }, "EBF site 113 (partition 1)":{ "attribute type":"branch label", "display order":115 }, "EBF site 117 (partition 1)":{ "attribute type":"branch label", "display order":119 }, "EBF site 12 (partition 1)":{ "attribute type":"branch label", "display order":14 }, "EBF site 136 (partition 1)":{ "attribute type":"branch label", "display order":138 }, "EBF site 140 (partition 1)":{ "attribute type":"branch label", "display order":142 }, "EBF site 142 (partition 1)":{ "attribute type":"branch label", "display order":144 }, "EBF site 145 (partition 1)":{ "attribute type":"branch label", "display order":147 }, "EBF site 146 (partition 1)":{ "attribute type":"branch label", "display order":148 }, "EBF site 152 (partition 1)":{ "attribute type":"branch label", "display order":154 }, "EBF site 153 (partition 1)":{ "attribute type":"branch label", "display order":155 }, "EBF site 154 (partition 1)":{ "attribute type":"branch label", "display order":156 }, "EBF site 155 (partition 1)":{ "attribute type":"branch label", "display order":157 }, "EBF site 156 (partition 1)":{ "attribute type":"branch label", "display order":158 }, "EBF site 157 (partition 1)":{ "attribute type":"branch label", "display order":159 }, "EBF site 16 (partition 1)":{ "attribute type":"branch label", "display order":18 }, "EBF site 167 (partition 1)":{ "attribute type":"branch label", "display order":169 }, "EBF site 170 (partition 1)":{ "attribute type":"branch label", "display order":172 }, "EBF site 171 (partition 1)":{ "attribute type":"branch label", "display order":173 }, "EBF site 172 (partition 1)":{ "attribute type":"branch label", "display order":174 }, "EBF site 175 (partition 1)":{ "attribute type":"branch label", "display order":177 }, "EBF site 178 (partition 1)":{ "attribute type":"branch label", "display order":180 }, "EBF site 181 (partition 1)":{ "attribute type":"branch label", "display order":183 }, "EBF site 196 (partition 1)":{ "attribute type":"branch label", "display order":198 }, "EBF site 197 (partition 1)":{ "attribute type":"branch label", "display order":199 }, "EBF site 200 (partition 1)":{ "attribute type":"branch label", "display order":202 }, "EBF site 204 (partition 1)":{ "attribute type":"branch label", "display order":206 }, "EBF site 206 (partition 1)":{ "attribute type":"branch label", "display order":208 }, "EBF site 209 (partition 1)":{ "attribute type":"branch label", "display order":211 }, "EBF site 21 (partition 1)":{ "attribute type":"branch label", "display order":23 }, "EBF site 213 (partition 1)":{ "attribute type":"branch label", "display order":215 }, "EBF site 217 (partition 1)":{ "attribute type":"branch label", "display order":219 }, "EBF site 228 (partition 1)":{ "attribute type":"branch label", "display order":230 }, "EBF site 237 (partition 1)":{ "attribute type":"branch label", "display order":239 }, "EBF site 241 (partition 1)":{ "attribute type":"branch label", "display order":243 }, "EBF site 250 (partition 1)":{ "attribute type":"branch label", "display order":252 }, "EBF site 254 (partition 1)":{ "attribute type":"branch label", "display order":256 }, "EBF site 256 (partition 1)":{ "attribute type":"branch label", "display order":258 }, "EBF site 258 (partition 1)":{ "attribute type":"branch label", "display order":260 }, "EBF site 278 (partition 1)":{ "attribute type":"branch label", "display order":280 }, "EBF site 279 (partition 1)":{ "attribute type":"branch label", "display order":281 }, "EBF site 28 (partition 1)":{ "attribute type":"branch label", "display order":30 }, "EBF site 288 (partition 1)":{ "attribute type":"branch label", "display order":290 }, "EBF site 298 (partition 1)":{ "attribute type":"branch label", "display order":300 }, "EBF site 3 (partition 1)":{ "attribute type":"branch label", "display order":5 }, "EBF site 302 (partition 1)":{ "attribute type":"branch label", "display order":304 }, "EBF site 304 (partition 1)":{ "attribute type":"branch label", "display order":306 }, "EBF site 306 (partition 1)":{ "attribute type":"branch label", "display order":308 }, "EBF site 309 (partition 1)":{ "attribute type":"branch label", "display order":311 }, "EBF site 312 (partition 1)":{ "attribute type":"branch label", "display order":314 }, "EBF site 315 (partition 1)":{ "attribute type":"branch label", "display order":317 }, "EBF site 327 (partition 1)":{ "attribute type":"branch label", "display order":329 }, "EBF site 329 (partition 1)":{ "attribute type":"branch label", "display order":331 }, "EBF site 332 (partition 1)":{ "attribute type":"branch label", "display order":334 }, "EBF site 336 (partition 1)":{ "attribute type":"branch label", "display order":338 }, "EBF site 341 (partition 1)":{ "attribute type":"branch label", "display order":343 }, "EBF site 342 (partition 1)":{ "attribute type":"branch label", "display order":344 }, "EBF site 348 (partition 1)":{ "attribute type":"branch label", "display order":350 }, "EBF site 351 (partition 1)":{ "attribute type":"branch label", "display order":353 }, "EBF site 353 (partition 1)":{ "attribute type":"branch label", "display order":355 }, "EBF site 354 (partition 1)":{ "attribute type":"branch label", "display order":356 }, "EBF site 361 (partition 1)":{ "attribute type":"branch label", "display order":363 }, "EBF site 362 (partition 1)":{ "attribute type":"branch label", "display order":364 }, "EBF site 369 (partition 1)":{ "attribute type":"branch label", "display order":371 }, "EBF site 379 (partition 1)":{ "attribute type":"branch label", "display order":381 }, "EBF site 389 (partition 1)":{ "attribute type":"branch label", "display order":391 }, "EBF site 417 (partition 1)":{ "attribute type":"branch label", "display order":419 }, "EBF site 424 (partition 1)":{ "attribute type":"branch label", "display order":426 }, "EBF site 431 (partition 1)":{ "attribute type":"branch label", "display order":433 }, "EBF site 433 (partition 1)":{ "attribute type":"branch label", "display order":435 }, "EBF site 441 (partition 1)":{ "attribute type":"branch label", "display order":443 }, "EBF site 445 (partition 1)":{ "attribute type":"branch label", "display order":447 }, "EBF site 45 (partition 1)":{ "attribute type":"branch label", "display order":47 }, "EBF site 466 (partition 1)":{ "attribute type":"branch label", "display order":468 }, "EBF site 477 (partition 1)":{ "attribute type":"branch label", "display order":479 }, "EBF site 488 (partition 1)":{ "attribute type":"branch label", "display order":490 }, "EBF site 489 (partition 1)":{ "attribute type":"branch label", "display order":491 }, "EBF site 499 (partition 1)":{ "attribute type":"branch label", "display order":501 }, "EBF site 50 (partition 1)":{ "attribute type":"branch label", "display order":52 }, "EBF site 506 (partition 1)":{ "attribute type":"branch label", "display order":508 }, "EBF site 509 (partition 1)":{ "attribute type":"branch label", "display order":511 }, "EBF site 515 (partition 1)":{ "attribute type":"branch label", "display order":517 }, "EBF site 52 (partition 1)":{ "attribute type":"branch label", "display order":54 }, "EBF site 527 (partition 1)":{ "attribute type":"branch label", "display order":529 }, "EBF site 529 (partition 1)":{ "attribute type":"branch label", "display order":531 }, "EBF site 537 (partition 1)":{ "attribute type":"branch label", "display order":539 }, "EBF site 539 (partition 1)":{ "attribute type":"branch label", "display order":541 }, "EBF site 545 (partition 1)":{ "attribute type":"branch label", "display order":547 }, "EBF site 549 (partition 1)":{ "attribute type":"branch label", "display order":551 }, "EBF site 553 (partition 1)":{ "attribute type":"branch label", "display order":555 }, "EBF site 558 (partition 1)":{ "attribute type":"branch label", "display order":560 }, "EBF site 560 (partition 1)":{ "attribute type":"branch label", "display order":562 }, "EBF site 564 (partition 1)":{ "attribute type":"branch label", "display order":566 }, "EBF site 58 (partition 1)":{ "attribute type":"branch label", "display order":60 }, "EBF site 59 (partition 1)":{ "attribute type":"branch label", "display order":61 }, "EBF site 60 (partition 1)":{ "attribute type":"branch label", "display order":62 }, "EBF site 68 (partition 1)":{ "attribute type":"branch label", "display order":70 }, "EBF site 69 (partition 1)":{ "attribute type":"branch label", "display order":71 }, "EBF site 78 (partition 1)":{ "attribute type":"branch label", "display order":80 }, "EBF site 79 (partition 1)":{ "attribute type":"branch label", "display order":81 }, "EBF site 8 (partition 1)":{ "attribute type":"branch label", "display order":10 }, "EBF site 84 (partition 1)":{ "attribute type":"branch label", "display order":86 }, "EBF site 86 (partition 1)":{ "attribute type":"branch label", "display order":88 }, "EBF site 89 (partition 1)":{ "attribute type":"branch label", "display order":91 }, "Global MG94xREV":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "original name":{ "attribute type":"node label", "display order":-1 } } }, "data partitions":{ "0":{ "coverage": [ [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, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565] ], "name":"meme.filter.default" } }, "fits":{ "Global MG94xREV":{ "AIC-c":6011.13695012892, "Equilibrium frequencies": [ [0.0487448731499957], [0.02916309663834602], [0.03100171502919514], [0.03392179881163448], [0.02040080210426937], [0.01220539771302355], [0.01297489997065711], [0.01419701929364967], [0.02306796533539959], [0.0138011088931582], [0.01467121445635504], [0.01605311140503505], [0.03067687144383888], [0.01835336741416609], [0.01951047494908151], [0.02134818687672324], [0.02126077850204813], [0.01271990463804815], [0.01352184453103644], [0.01479548113102975], [0.008898103672735205], [0.005323560008197935], [0.005659189501089015], [0.006192234446128948], [0.010061425331433], [0.006019552422614294], [0.006399061496227086], [0.007001795754005012], [0.01338015932252603], [0.008005085543223482], [0.008509774660521757], [0.009311319186526256], [0.04013232935583105], [0.02401038147590574], [0.02552414146855538], [0.02792828690027832], [0.01679626299677307], [0.01004887302569606], [0.0106824148947738], [0.01168860266413242], [0.01899217543474583], [0.01136264414662781], [0.01207901411089265], [0.0132167490129733], [0.02525669324448205], [0.01511058165209229], [0.0160632443156804], [0.01757625800461362], [0.02112670632168297], [0.02457406668036405], [0.01477901198657192], [0.008841991514828857], [0.009399444257673735], [0.01028478768834936], [0.009997977173519282], [0.01062831025955897], [0.01162940185705429], [0.02222333457585675], [0.01329578296096281], [0.01413402971424556], [0.01546532867335853] ], "Log Likelihood":-2978.298667783946, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *test*": [ [0.2932353608697501, 1] ] }, "display order":1, "estimated parameters":27 }, "Nucleotide GTR":{ "AIC-c":6152.529196194525, "Equilibrium frequencies": [ [0.3478363400542389], [0.184883858035609], [0.2307510906732697], [0.2365287112368824] ], "Log Likelihood":-3056.215005465311, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0.1810796022573985, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.08708610799393901, "Substitution rate from nucleotide C to nucleotide G":0.02931879134098465, "Substitution rate from nucleotide C to nucleotide T":1.419136867291551, "Substitution rate from nucleotide G to nucleotide T":0.1065442350926398 }, "display order":0, "estimated parameters":20 } }, "input":{ "file name":"/tmp/tmpdqyv1aux/job_working_directory/000/3/working/./meme_input.fa", "number of sequences":5, "number of sites":566, "partition count":1, "trees":{ "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:-1)Node3:0.003130608143291779,(CK_HK_WF157_2003:0.00663129750258774)Node9:0.004655295319725731)Node2:0.0116808817874948,(MALLARD_VIETNAM_16_2003:0.003244216605281072)Node11:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)" } }, "tested":{ "0":{ "CHICKEN_CK_160_2005":"test", "CHICKEN_HEBEI_326_2005":"test", "CK_HK_WF157_2003":"test", "MALLARD_VIETNAM_16_2003":"test", "Node11":"test", "Node2":"test", "Node3":"test", "Node4":"test", "Node5":"test", "Node7":"test", "Node9":"test", "SWINE_ANHUI_1_2004":"test" } }, "timers":{ "MEME analysis":{ "order":2, "timer":437 }, "Model fitting":{ "order":1, "timer":4 }, "Total time":{ "order":0, "timer":442 } } }