Mercurial > repos > iuc > hyphy_slac
diff test-data/meme-out1.json @ 1:c2bed8cc8fc1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
| author | iuc |
|---|---|
| date | Wed, 21 Aug 2019 12:27:21 -0400 |
| parents | 9da003917dcb |
| children | 25782236e47e |
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--- a/test-data/meme-out1.json Thu Jan 17 04:24:25 2019 -0500 +++ b/test-data/meme-out1.json Wed Aug 21 12:27:21 2019 -0400 @@ -1,849 +1,748 @@ { - "analysis":{ - "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 ", - "version":"2.0.1", - "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", - "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", - "contact":"spond@temple.edu", - "requirements":"in-frame codon alignment and a phylogenetic tree" - }, - "fits":{ - "Nucleotide GTR":{ - "Log Likelihood":-4394.17778442101, - "estimated parameters":47, - "AIC-c":8882.482274823486, - "Equilibrium frequencies":[ - [0.3460163217230355], - [0.1876507375623983], - [0.2296889898480005], - [0.2366439508665657] - ], - "Rate Distributions":{ - "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088, - "Substitution rate from nucleotide A to nucleotide G":1, - "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337, - "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039, - "Substitution rate from nucleotide C to nucleotide T":1.290725939052547, - "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102 - }, - "display order":0 + "MLE":{ + "content":{ + "0": [ +[0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 0, 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<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"] + ] }, - "timers":{ - "Total time":{ - "timer":816, - "order":0 - }, - "Model fitting":{ - "timer":12, - "order":1 - }, - "MEME analysis":{ - "timer":803, - "order":2 - } - }, - "tested":{ - "0":{ - "TREESPARROW_HENAN_1_2004":"test", - "TREESPARROW_HENAN_3_2004":"test", - "Node6":"test", - "TREESPARROW_HENAN_4_2004":"test", - "Node5":"test", - "CHICKEN_HEBEI_326_2005":"test", - "SWINE_ANHUI_1_2004":"test", - "TREESPARROW_HENAN_2_2004":"test", - "Node12":"test", - "Node10":"test", - 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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":{ - "TREESPARROW_HENAN_1_2004":{ - "original name":"TREESPARROW_HENAN_1_2004", - "Nucleotide GTR":0.01066479252384179, - "Global MG94xREV":0.01076673590455662, - "EBF site 3 (partition 1)":0.9456096051294662, - "EBF site 8 (partition 1)":1162.743096991633, - "EBF site 9 (partition 1)":1, - "EBF site 10 (partition 1)":218.8691185742497, - "EBF site 11 (partition 1)":127.9229379574454, - "EBF site 12 (partition 1)":1, - "EBF site 16 (partition 1)":0.9451095622554209, - "EBF site 17 (partition 1)":1, - "EBF site 20 (partition 1)":3527.455058707973, - "EBF site 21 (partition 1)":176.9630563981623, - "EBF site 26 (partition 1)":408.9192237736214, - "EBF site 27 (partition 1)":6018.398467534517, - "EBF site 28 (partition 1)":1, - "EBF site 32 (partition 1)":3526.472765483446, 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+ "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 494 (partition 1)":{ + "attribute type":"branch label", + "display order":496 + }, + "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 507 (partition 1)":{ + "attribute type":"branch label", + "display order":509 + }, + "EBF site 509 (partition 1)":{ + "attribute type":"branch label", + "display order":511 + }, "EBF site 51 (partition 1)":{ "attribute type":"branch label", "display order":53 }, + "EBF site 513 (partition 1)":{ + "attribute type":"branch label", + "display order":515 + }, + "EBF site 514 (partition 1)":{ + "attribute type":"branch label", + "display order":516 + }, + "EBF site 515 (partition 1)":{ + "attribute type":"branch label", + "display order":517 + }, + "EBF site 519 (partition 1)":{ + "attribute type":"branch label", + "display order":521 + }, "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 54 (partition 1)":{ "attribute type":"branch label", "display order":56 }, + "EBF site 540 (partition 1)":{ + "attribute type":"branch label", + "display order":542 + }, + "EBF site 544 (partition 1)":{ + "attribute type":"branch label", + "display order":546 + }, + "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 @@ -8556,9 +6035,9 @@ "attribute type":"branch label", "display order":81 }, - "EBF site 80 (partition 1)":{ - "attribute type":"branch label", - "display order":82 + "EBF site 8 (partition 1)":{ + "attribute type":"branch label", + "display order":10 }, "EBF site 81 (partition 1)":{ "attribute type":"branch label", @@ -8576,1241 +6055,185 @@ "attribute type":"branch label", "display order":91 }, - "EBF site 91 (partition 1)":{ - "attribute type":"branch label", - "display order":93 + "EBF site 9 (partition 1)":{ + "attribute type":"branch label", + "display order":11 }, "EBF site 99 (partition 1)":{ "attribute type":"branch label", "display order":101 }, - "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 107 (partition 1)":{ - "attribute type":"branch label", - "display order":109 - }, - "EBF site 109 (partition 1)":{ - "attribute type":"branch label", - "display order":111 - }, - "EBF site 110 (partition 1)":{ - "attribute type":"branch label", - "display order":112 - }, - "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 128 (partition 1)":{ - "attribute type":"branch label", - "display order":130 - }, - "EBF site 131 (partition 1)":{ - "attribute type":"branch label", - "display order":133 - }, - "EBF site 136 (partition 1)":{ - "attribute type":"branch label", - "display order":138 - }, - "EBF site 139 (partition 1)":{ - "attribute type":"branch label", - "display order":141 - }, - "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 143 (partition 1)":{ - "attribute type":"branch label", - "display order":145 - }, - "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 147 (partition 1)":{ - "attribute type":"branch label", - "display order":149 - }, - "EBF site 150 (partition 1)":{ - "attribute type":"branch label", - "display order":152 - }, - "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 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 173 (partition 1)":{ - "attribute type":"branch label", - "display order":175 - }, - "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 179 (partition 1)":{ - "attribute type":"branch label", - "display order":181 - }, - "EBF site 181 (partition 1)":{ - "attribute type":"branch label", - "display order":183 - }, - "EBF site 185 (partition 1)":{ - "attribute type":"branch label", - "display order":187 - }, - "EBF site 191 (partition 1)":{ - "attribute type":"branch label", - "display order":193 - }, - "EBF site 195 (partition 1)":{ - "attribute type":"branch label", - "display order":197 - }, - "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 201 (partition 1)":{ - "attribute type":"branch label", - "display order":203 - }, - "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 211 (partition 1)":{ - "attribute type":"branch label", - "display order":213 - }, - "EBF site 212 (partition 1)":{ - "attribute type":"branch label", - "display order":214 - }, - "EBF site 213 (partition 1)":{ - "attribute type":"branch label", - "display order":215 - }, - "EBF site 214 (partition 1)":{ - "attribute type":"branch label", - "display order":216 - }, - "EBF site 217 (partition 1)":{ - "attribute type":"branch label", - "display order":219 - }, - "EBF site 221 (partition 1)":{ - "attribute type":"branch label", - "display order":223 - }, - "EBF site 222 (partition 1)":{ - "attribute type":"branch label", - "display order":224 - }, - "EBF site 224 (partition 1)":{ - "attribute type":"branch label", - "display order":226 - }, - "EBF site 226 (partition 1)":{ - "attribute type":"branch label", - "display order":228 - }, - "EBF site 228 (partition 1)":{ - "attribute type":"branch label", - "display order":230 - }, - "EBF site 230 (partition 1)":{ - "attribute type":"branch label", - "display order":232 - }, - "EBF site 231 (partition 1)":{ - "attribute type":"branch label", - "display order":233 - }, - "EBF site 233 (partition 1)":{ - "attribute type":"branch label", - "display order":235 - }, - "EBF site 235 (partition 1)":{ - "attribute type":"branch label", - "display order":237 - }, - "EBF site 236 (partition 1)":{ - "attribute type":"branch label", - "display order":238 - }, - "EBF site 237 (partition 1)":{ - "attribute type":"branch label", - "display order":239 - }, - "EBF site 240 (partition 1)":{ - "attribute type":"branch label", - "display order":242 - }, - "EBF site 241 (partition 1)":{ - "attribute type":"branch label", - "display order":243 - }, - "EBF site 242 (partition 1)":{ - "attribute type":"branch label", - "display order":244 - }, - "EBF site 250 (partition 1)":{ - "attribute type":"branch label", - "display order":252 - }, - "EBF site 253 (partition 1)":{ - "attribute type":"branch label", - "display order":255 - }, - "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 265 (partition 1)":{ - "attribute type":"branch label", - "display order":267 - }, - "EBF site 268 (partition 1)":{ - "attribute type":"branch label", - "display order":270 - }, - "EBF site 271 (partition 1)":{ - "attribute type":"branch label", - "display order":273 - }, - "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 282 (partition 1)":{ - "attribute type":"branch label", - "display order":284 - }, - "EBF site 283 (partition 1)":{ - "attribute type":"branch label", - "display order":285 - }, - "EBF site 288 (partition 1)":{ - "attribute type":"branch label", - "display order":290 - }, - "EBF site 291 (partition 1)":{ - "attribute type":"branch label", - "display order":293 - }, - "EBF site 293 (partition 1)":{ - "attribute type":"branch label", - "display order":295 - }, - "EBF site 296 (partition 1)":{ - "attribute type":"branch label", - "display order":298 - }, - "EBF site 298 (partition 1)":{ - "attribute type":"branch label", - "display order":300 - }, - "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 311 (partition 1)":{ - "attribute type":"branch label", - "display order":313 - }, - "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 317 (partition 1)":{ - "attribute type":"branch label", - "display order":319 - }, - "EBF site 327 (partition 1)":{ - "attribute type":"branch label", - "display order":329 - }, - "EBF site 328 (partition 1)":{ - "attribute type":"branch label", - "display order":330 - }, - "EBF site 329 (partition 1)":{ - "attribute type":"branch label", - "display order":331 - }, - "EBF site 331 (partition 1)":{ - "attribute type":"branch label", - "display order":333 - }, - "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 338 (partition 1)":{ - "attribute type":"branch label", - "display order":340 - }, - "EBF site 339 (partition 1)":{ - "attribute type":"branch label", - "display order":341 - }, - "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 344 (partition 1)":{ - "attribute type":"branch label", - "display order":346 - }, - "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 357 (partition 1)":{ - "attribute type":"branch label", - "display order":359 - }, - "EBF site 358 (partition 1)":{ - "attribute type":"branch label", - "display order":360 - }, - "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 375 (partition 1)":{ - "attribute type":"branch label", - "display order":377 - }, - "EBF site 377 (partition 1)":{ - "attribute type":"branch label", - "display order":379 - }, - "EBF site 379 (partition 1)":{ - "attribute type":"branch label", - "display order":381 - }, - "EBF site 433 (partition 1)":{ - "attribute type":"branch label", - "display order":435 - }, - "EBF site 384 (partition 1)":{ - "attribute type":"branch label", - "display order":386 - }, - "EBF site 389 (partition 1)":{ - "attribute type":"branch label", - "display order":391 - }, - "EBF site 403 (partition 1)":{ - "attribute type":"branch label", - "display order":405 - }, - "EBF site 408 (partition 1)":{ - "attribute type":"branch label", - "display order":410 - }, - "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 429 (partition 1)":{ - "attribute type":"branch label", - "display order":431 - }, - "EBF site 431 (partition 1)":{ - "attribute type":"branch label", - "display order":433 - }, - "EBF site 440 (partition 1)":{ - "attribute type":"branch label", - "display order":442 - }, - "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 454 (partition 1)":{ - "attribute type":"branch label", - "display order":456 - }, - "EBF site 462 (partition 1)":{ - "attribute type":"branch label", - "display order":464 - }, - "EBF site 466 (partition 1)":{ - "attribute type":"branch label", - "display order":468 - }, - "EBF site 471 (partition 1)":{ - "attribute type":"branch label", - "display order":473 - }, - "EBF site 473 (partition 1)":{ - "attribute type":"branch label", - "display order":475 - }, - "EBF site 477 (partition 1)":{ - "attribute type":"branch label", - "display order":479 - }, - "EBF site 478 (partition 1)":{ - "attribute type":"branch label", - "display order":480 - }, - "EBF site 485 (partition 1)":{ - "attribute type":"branch label", - "display order":487 - }, - "EBF site 479 (partition 1)":{ - "attribute type":"branch label", - "display order":481 - }, - "EBF site 481 (partition 1)":{ - "attribute type":"branch label", - "display order":483 - }, - "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 492 (partition 1)":{ - "attribute type":"branch label", - "display order":494 - }, - "EBF site 494 (partition 1)":{ - "attribute type":"branch label", - "display order":496 - }, - "EBF site 499 (partition 1)":{ - "attribute type":"branch label", - "display order":501 - }, - "EBF site 500 (partition 1)":{ - "attribute type":"branch label", - "display order":502 - }, - "EBF site 506 (partition 1)":{ - "attribute type":"branch label", - "display order":508 - }, - "EBF site 507 (partition 1)":{ - "attribute type":"branch label", - "display order":509 - }, - "EBF site 508 (partition 1)":{ - "attribute type":"branch label", - "display order":510 - }, - "EBF site 509 (partition 1)":{ - "attribute type":"branch label", - "display order":511 - }, - "EBF site 513 (partition 1)":{ - "attribute type":"branch label", - "display order":515 - }, - "EBF site 514 (partition 1)":{ - "attribute type":"branch label", - "display order":516 - }, - "EBF site 515 (partition 1)":{ - "attribute type":"branch label", - "display order":517 - }, - "EBF site 519 (partition 1)":{ - "attribute type":"branch label", - "display order":521 - }, - "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 538 (partition 1)":{ - "attribute type":"branch label", - "display order":540 - }, - "EBF site 539 (partition 1)":{ - "attribute type":"branch label", - "display order":541 - }, - "EBF site 540 (partition 1)":{ - "attribute type":"branch label", - "display order":542 - }, - "EBF site 544 (partition 1)":{ - "attribute type":"branch label", - "display order":546 - }, - "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 + "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 } } }, - "MLE":{ - "headers":[ - ["alpha;", "Synonymous substitution rate at a site"], - ["β<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"], - ["p<sup>-</sup>", "Mixture distribution weight allocated to β<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"], - ["β<sup>+</sup>", "Non-synonymous substitution rate 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"] - ], - "content":{ - "0":[ - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [3.518153136581004e-17, 3.243045519502881e-17, 1.022166200682819e-08, 1.291751771813077, 0.999999989778338, 0.5894186108086057, 0.4058674930166563, 1, 0.3590955405423049], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1.015244473805534e-08, 2.805293595854978, 0.9999999898475552, 1.564165559839974, 0.2310493931422519, 2, 0.7798467493791119], - [3.097517451103013, 3.633546560692318e-13, 0.006739028294327419, 0, 0.9932609717056726, 0, 0.6666666666666666, 0, 0.3592491319023247], - [0, 0, 1.066894692458495e-08, 2.051552228725943, 0.9999999893310531, 0.4229558324457479, 0.4514150344986089, 1, 0.5703133313001572], - [0, 0, 1.001269178443788e-08, 3.944223233914665, 0.9999999899873082, 2.43042776936683, 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