Mercurial > repos > iuc > hyphy_prime

comparison test-data/meme-out1.json @ 0:725ef5f6d749 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
author iuc
date Fri, 27 Mar 2020 13:15:01 -0400
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children
comparison
equal deleted inserted replaced
-1:000000000000 0:725ef5f6d749
1 {
2 "MLE":{
3 "content":{
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572 },
573 "headers": [
574 ["alpha;", "Synonymous substitution rate at a site"],
575 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
576 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
577 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
578 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
579 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
580 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
581 ["# 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 &beta;<sup>+</sup> rate"],
582 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
583 ]
584 },
585 "analysis":{
586 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
587 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
588 "contact":"spond@temple.edu",
589 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (&alpha;) and a two-category mixture of non-synonymous\n (&beta;-, with proportion p-, and &beta;+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if &beta;+ > &alpha; 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 ",
590 "requirements":"in-frame codon alignment and a phylogenetic tree",
591 "version":"2.1.1"
592 },
593 "branch attributes":{
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1942 "original name":"SWINE_ANHUI_1_2004"
1943 }
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2137 },
2138 "EBF site 3 (partition 1)":{
2139 "attribute type":"branch label",
2140 "display order":5
2141 },
2142 "EBF site 302 (partition 1)":{
2143 "attribute type":"branch label",
2144 "display order":304
2145 },
2146 "EBF site 304 (partition 1)":{
2147 "attribute type":"branch label",
2148 "display order":306
2149 },
2150 "EBF site 306 (partition 1)":{
2151 "attribute type":"branch label",
2152 "display order":308
2153 },
2154 "EBF site 309 (partition 1)":{
2155 "attribute type":"branch label",
2156 "display order":311
2157 },
2158 "EBF site 312 (partition 1)":{
2159 "attribute type":"branch label",
2160 "display order":314
2161 },
2162 "EBF site 315 (partition 1)":{
2163 "attribute type":"branch label",
2164 "display order":317
2165 },
2166 "EBF site 327 (partition 1)":{
2167 "attribute type":"branch label",
2168 "display order":329
2169 },
2170 "EBF site 329 (partition 1)":{
2171 "attribute type":"branch label",
2172 "display order":331
2173 },
2174 "EBF site 332 (partition 1)":{
2175 "attribute type":"branch label",
2176 "display order":334
2177 },
2178 "EBF site 336 (partition 1)":{
2179 "attribute type":"branch label",
2180 "display order":338
2181 },
2182 "EBF site 341 (partition 1)":{
2183 "attribute type":"branch label",
2184 "display order":343
2185 },
2186 "EBF site 342 (partition 1)":{
2187 "attribute type":"branch label",
2188 "display order":344
2189 },
2190 "EBF site 348 (partition 1)":{
2191 "attribute type":"branch label",
2192 "display order":350
2193 },
2194 "EBF site 351 (partition 1)":{
2195 "attribute type":"branch label",
2196 "display order":353
2197 },
2198 "EBF site 353 (partition 1)":{
2199 "attribute type":"branch label",
2200 "display order":355
2201 },
2202 "EBF site 354 (partition 1)":{
2203 "attribute type":"branch label",
2204 "display order":356
2205 },
2206 "EBF site 361 (partition 1)":{
2207 "attribute type":"branch label",
2208 "display order":363
2209 },
2210 "EBF site 362 (partition 1)":{
2211 "attribute type":"branch label",
2212 "display order":364
2213 },
2214 "EBF site 369 (partition 1)":{
2215 "attribute type":"branch label",
2216 "display order":371
2217 },
2218 "EBF site 379 (partition 1)":{
2219 "attribute type":"branch label",
2220 "display order":381
2221 },
2222 "EBF site 389 (partition 1)":{
2223 "attribute type":"branch label",
2224 "display order":391
2225 },
2226 "EBF site 417 (partition 1)":{
2227 "attribute type":"branch label",
2228 "display order":419
2229 },
2230 "EBF site 424 (partition 1)":{
2231 "attribute type":"branch label",
2232 "display order":426
2233 },
2234 "EBF site 431 (partition 1)":{
2235 "attribute type":"branch label",
2236 "display order":433
2237 },
2238 "EBF site 433 (partition 1)":{
2239 "attribute type":"branch label",
2240 "display order":435
2241 },
2242 "EBF site 441 (partition 1)":{
2243 "attribute type":"branch label",
2244 "display order":443
2245 },
2246 "EBF site 445 (partition 1)":{
2247 "attribute type":"branch label",
2248 "display order":447
2249 },
2250 "EBF site 45 (partition 1)":{
2251 "attribute type":"branch label",
2252 "display order":47
2253 },
2254 "EBF site 466 (partition 1)":{
2255 "attribute type":"branch label",
2256 "display order":468
2257 },
2258 "EBF site 477 (partition 1)":{
2259 "attribute type":"branch label",
2260 "display order":479
2261 },
2262 "EBF site 488 (partition 1)":{
2263 "attribute type":"branch label",
2264 "display order":490
2265 },
2266 "EBF site 489 (partition 1)":{
2267 "attribute type":"branch label",
2268 "display order":491
2269 },
2270 "EBF site 499 (partition 1)":{
2271 "attribute type":"branch label",
2272 "display order":501
2273 },
2274 "EBF site 50 (partition 1)":{
2275 "attribute type":"branch label",
2276 "display order":52
2277 },
2278 "EBF site 506 (partition 1)":{
2279 "attribute type":"branch label",
2280 "display order":508
2281 },
2282 "EBF site 509 (partition 1)":{
2283 "attribute type":"branch label",
2284 "display order":511
2285 },
2286 "EBF site 515 (partition 1)":{
2287 "attribute type":"branch label",
2288 "display order":517
2289 },
2290 "EBF site 52 (partition 1)":{
2291 "attribute type":"branch label",
2292 "display order":54
2293 },
2294 "EBF site 527 (partition 1)":{
2295 "attribute type":"branch label",
2296 "display order":529
2297 },
2298 "EBF site 529 (partition 1)":{
2299 "attribute type":"branch label",
2300 "display order":531
2301 },
2302 "EBF site 537 (partition 1)":{
2303 "attribute type":"branch label",
2304 "display order":539
2305 },
2306 "EBF site 539 (partition 1)":{
2307 "attribute type":"branch label",
2308 "display order":541
2309 },
2310 "EBF site 545 (partition 1)":{
2311 "attribute type":"branch label",
2312 "display order":547
2313 },
2314 "EBF site 549 (partition 1)":{
2315 "attribute type":"branch label",
2316 "display order":551
2317 },
2318 "EBF site 553 (partition 1)":{
2319 "attribute type":"branch label",
2320 "display order":555
2321 },
2322 "EBF site 558 (partition 1)":{
2323 "attribute type":"branch label",
2324 "display order":560
2325 },
2326 "EBF site 560 (partition 1)":{
2327 "attribute type":"branch label",
2328 "display order":562
2329 },
2330 "EBF site 564 (partition 1)":{
2331 "attribute type":"branch label",
2332 "display order":566
2333 },
2334 "EBF site 58 (partition 1)":{
2335 "attribute type":"branch label",
2336 "display order":60
2337 },
2338 "EBF site 59 (partition 1)":{
2339 "attribute type":"branch label",
2340 "display order":61
2341 },
2342 "EBF site 60 (partition 1)":{
2343 "attribute type":"branch label",
2344 "display order":62
2345 },
2346 "EBF site 68 (partition 1)":{
2347 "attribute type":"branch label",
2348 "display order":70
2349 },
2350 "EBF site 69 (partition 1)":{
2351 "attribute type":"branch label",
2352 "display order":71
2353 },
2354 "EBF site 78 (partition 1)":{
2355 "attribute type":"branch label",
2356 "display order":80
2357 },
2358 "EBF site 79 (partition 1)":{
2359 "attribute type":"branch label",
2360 "display order":81
2361 },
2362 "EBF site 8 (partition 1)":{
2363 "attribute type":"branch label",
2364 "display order":10
2365 },
2366 "EBF site 84 (partition 1)":{
2367 "attribute type":"branch label",
2368 "display order":86
2369 },
2370 "EBF site 86 (partition 1)":{
2371 "attribute type":"branch label",
2372 "display order":88
2373 },
2374 "EBF site 89 (partition 1)":{
2375 "attribute type":"branch label",
2376 "display order":91
2377 },
2378 "Global MG94xREV":{
2379 "attribute type":"branch length",
2380 "display order":1
2381 },
2382 "Nucleotide GTR":{
2383 "attribute type":"branch length",
2384 "display order":0
2385 },
2386 "original name":{
2387 "attribute type":"node label",
2388 "display order":-1
2389 }
2390 }
2391 },
2392 "data partitions":{
2393 "0":{
2394 "coverage": [
2395 [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]
2396 ],
2397 "name":"meme.filter.default"
2398 }
2399 },
2400 "fits":{
2401 "Global MG94xREV":{
2402 "AIC-c":6011.13695012892,
2403 "Equilibrium frequencies": [
2404 [0.0487448731499957],
2405 [0.02916309663834602],
2406 [0.03100171502919514],
2407 [0.03392179881163448],
2408 [0.02040080210426937],
2409 [0.01220539771302355],
2410 [0.01297489997065711],
2411 [0.01419701929364967],
2412 [0.02306796533539959],
2413 [0.0138011088931582],
2414 [0.01467121445635504],
2415 [0.01605311140503505],
2416 [0.03067687144383888],
2417 [0.01835336741416609],
2418 [0.01951047494908151],
2419 [0.02134818687672324],
2420 [0.02126077850204813],
2421 [0.01271990463804815],
2422 [0.01352184453103644],
2423 [0.01479548113102975],
2424 [0.008898103672735205],
2425 [0.005323560008197935],
2426 [0.005659189501089015],
2427 [0.006192234446128948],
2428 [0.010061425331433],
2429 [0.006019552422614294],
2430 [0.006399061496227086],
2431 [0.007001795754005012],
2432 [0.01338015932252603],
2433 [0.008005085543223482],
2434 [0.008509774660521757],
2435 [0.009311319186526256],
2436 [0.04013232935583105],
2437 [0.02401038147590574],
2438 [0.02552414146855538],
2439 [0.02792828690027832],
2440 [0.01679626299677307],
2441 [0.01004887302569606],
2442 [0.0106824148947738],
2443 [0.01168860266413242],
2444 [0.01899217543474583],
2445 [0.01136264414662781],
2446 [0.01207901411089265],
2447 [0.0132167490129733],
2448 [0.02525669324448205],
2449 [0.01511058165209229],
2450 [0.0160632443156804],
2451 [0.01757625800461362],
2452 [0.02112670632168297],
2453 [0.02457406668036405],
2454 [0.01477901198657192],
2455 [0.008841991514828857],
2456 [0.009399444257673735],
2457 [0.01028478768834936],
2458 [0.009997977173519282],
2459 [0.01062831025955897],
2460 [0.01162940185705429],
2461 [0.02222333457585675],
2462 [0.01329578296096281],
2463 [0.01413402971424556],
2464 [0.01546532867335853]
2465 ],
2466 "Log Likelihood":-2978.298667783946,
2467 "Rate Distributions":{
2468 "non-synonymous/synonymous rate ratio for *test*": [
2469 [0.2932353608697501, 1]
2470 ]
2471 },
2472 "display order":1,
2473 "estimated parameters":27
2474 },
2475 "Nucleotide GTR":{
2476 "AIC-c":6152.529196194525,
2477 "Equilibrium frequencies": [
2478 [0.3478363400542389],
2479 [0.184883858035609],
2480 [0.2307510906732697],
2481 [0.2365287112368824]
2482 ],
2483 "Log Likelihood":-3056.215005465311,
2484 "Rate Distributions":{
2485 "Substitution rate from nucleotide A to nucleotide C":0.1810796022573985,
2486 "Substitution rate from nucleotide A to nucleotide G":1,
2487 "Substitution rate from nucleotide A to nucleotide T":0.08708610799393901,
2488 "Substitution rate from nucleotide C to nucleotide G":0.02931879134098465,
2489 "Substitution rate from nucleotide C to nucleotide T":1.419136867291551,
2490 "Substitution rate from nucleotide G to nucleotide T":0.1065442350926398
2491 },
2492 "display order":0,
2493 "estimated parameters":20
2494 }
2495 },
2496 "input":{
2497 "file name":"/tmp/tmpdqyv1aux/job_working_directory/000/3/working/./meme_input.fa",
2498 "number of sequences":5,
2499 "number of sites":566,
2500 "partition count":1,
2501 "trees":{
2502 "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)"
2503 }
2504 },
2505 "tested":{
2506 "0":{
2507 "CHICKEN_CK_160_2005":"test",
2508 "CHICKEN_HEBEI_326_2005":"test",
2509 "CK_HK_WF157_2003":"test",
2510 "MALLARD_VIETNAM_16_2003":"test",
2511 "Node11":"test",
2512 "Node2":"test",
2513 "Node3":"test",
2514 "Node4":"test",
2515 "Node5":"test",
2516 "Node7":"test",
2517 "Node9":"test",
2518 "SWINE_ANHUI_1_2004":"test"
2519 }
2520 },
2521 "timers":{
2522 "MEME analysis":{
2523 "order":2,
2524 "timer":437
2525 },
2526 "Model fitting":{
2527 "order":1,
2528 "timer":4
2529 },
2530 "Total time":{
2531 "order":0,
2532 "timer":442
2533 }
2534 }
2535 }