Mercurial > repos > iuc > hyphy_fade
diff test-data/meme-out1.json @ 5:16b4a3869bd5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
| author | iuc |
|---|---|
| date | Thu, 20 Feb 2020 18:12:40 -0500 |
| parents | 6164d9298db9 |
| children |
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--- a/test-data/meme-out1.json Mon Feb 17 14:52:56 2020 -0500 +++ b/test-data/meme-out1.json Thu Feb 20 18:12:40 2020 -0500 @@ -4,568 +4,568 @@ "0": [ [0, 0, 1, 0, 0, 0, 1, 0, 0], [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 0, 1.817789942174416, 1, 0, 0.6666666666666666, 0, 0.1215618554703716], - [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, 0, 1.900735833403759, 1, 0, 0.6666666666666666, 0, 0.1271087320415013], - [4.223295318660594, 0, 0.1812832787403597, 0, 0.8187167212596403, 0, 0.6666666666666666, 0, 0.1220041843130002], - [0, 0, 0, 1.454313013998262, 1, 0, 0.6666666666666666, 0, 0.0972549051541481], - [0, 0, 0, 3.87077558632765, 1, 0, 0.6666666666666666, 0, 0.2588520551613089], - [5.621376790757513, 1.370160457631764, 0.9999999999999731, 0.7647952134694137, 2.686739719592879e-14, 0, 0.6666666666666666, 0, 0.254019836850675], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1, 0, 0, 0, 1, 0, 0], - [0, 0, 1, 0, 0, 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"EBF site 200 (partition 1)":1, @@ -808,206 +627,20 @@ "EBF site 206 (partition 1)":1, "EBF site 209 (partition 1)":1, "EBF site 21 (partition 1)":1, - "EBF site 211 (partition 1)":0.6737403783181751, "EBF site 213 (partition 1)":1, - "EBF site 214 (partition 1)":0.1418107606887018, "EBF site 217 (partition 1)":1, - "EBF site 221 (partition 1)":1, - "EBF site 222 (partition 1)":1, - "EBF site 224 (partition 1)":1, - "EBF site 226 (partition 1)":1, "EBF site 228 (partition 1)":1, - "EBF site 230 (partition 1)":1, - "EBF site 231 (partition 1)":1, - "EBF site 233 (partition 1)":1, "EBF site 237 (partition 1)":1, - "EBF site 240 (partition 1)":1, "EBF site 241 (partition 1)":1, "EBF site 250 (partition 1)":1, "EBF site 254 (partition 1)":1, "EBF site 256 (partition 1)":1, "EBF site 258 (partition 1)":1, - "EBF site 265 (partition 1)":1, - "EBF site 271 (partition 1)":1, "EBF site 278 (partition 1)":1, "EBF site 279 (partition 1)":1, "EBF site 28 (partition 1)":1, - "EBF site 283 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(partition 1)":1, + "CHICKEN_HEBEI_326_2005":{ "EBF site 100 (partition 1)":1, - "EBF site 102 (partition 1)":1379.756035017705, + "EBF site 102 (partition 1)":0.06569877494136181, "EBF site 104 (partition 1)":1, - "EBF site 107 (partition 1)":1, - "EBF site 109 (partition 1)":1, "EBF site 11 (partition 1)":1, - "EBF site 110 (partition 1)":1, "EBF site 112 (partition 1)":1, "EBF site 113 (partition 1)":1, "EBF site 117 (partition 1)":1, @@ -1124,27 +717,22 @@ "EBF site 136 (partition 1)":1, "EBF site 140 (partition 1)":1, "EBF site 142 (partition 1)":1, - "EBF site 145 (partition 1)":0.9437923890358962, + "EBF site 145 (partition 1)":1, "EBF site 146 (partition 1)":1, - "EBF site 147 (partition 1)":1, - "EBF site 150 (partition 1)":0.8851921878588614, "EBF site 152 (partition 1)":1, "EBF site 153 (partition 1)":1, - "EBF site 154 (partition 1)":0.6798007785957374, + "EBF site 154 (partition 1)":1, "EBF site 155 (partition 1)":1, "EBF site 156 (partition 1)":1, "EBF site 157 (partition 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(partition 1)":1, - "EBF site 224 (partition 1)":1, - "EBF site 226 (partition 1)":1, "EBF site 228 (partition 1)":1, - "EBF site 230 (partition 1)":1, - "EBF site 231 (partition 1)":1, - "EBF site 233 (partition 1)":1, "EBF site 237 (partition 1)":1, - "EBF site 240 (partition 1)":1, "EBF site 241 (partition 1)":1, "EBF site 250 (partition 1)":1, "EBF site 254 (partition 1)":1, "EBF site 256 (partition 1)":1, "EBF site 258 (partition 1)":1, - "EBF site 265 (partition 1)":1, - "EBF site 271 (partition 1)":1, "EBF site 278 (partition 1)":1, "EBF site 279 (partition 1)":1, "EBF site 28 (partition 1)":1, - "EBF site 283 (partition 1)":1, "EBF site 288 (partition 1)":1, - "EBF site 291 (partition 1)":1, - "EBF site 298 (partition 1)":0.9316810582498189, + "EBF site 298 (partition 1)":0.5638294970328166, "EBF site 3 (partition 1)":1, "EBF site 302 (partition 1)":1, "EBF site 304 (partition 1)":1, @@ -1188,107 +762,67 @@ "EBF site 312 (partition 1)":1, "EBF site 315 (partition 1)":1, "EBF site 327 (partition 1)":1, - "EBF site 328 (partition 1)":1, "EBF site 329 (partition 1)":1, - "EBF site 33 (partition 1)":1, "EBF site 332 (partition 1)":1, - "EBF site 336 (partition 1)":0.04728563578028874, - "EBF site 338 (partition 1)":0.6046360278098571, - "EBF site 339 (partition 1)":1, - "EBF site 341 (partition 1)":1, + "EBF site 336 (partition 1)":0.02455830900453714, + "EBF site 341 (partition 1)":0.3158303901000457, "EBF site 342 (partition 1)":1, - "EBF site 344 (partition 1)":1, "EBF site 348 (partition 1)":1, "EBF site 351 (partition 1)":1, "EBF site 353 (partition 1)":1, "EBF site 354 (partition 1)":1, - "EBF site 357 (partition 1)":1, "EBF site 361 (partition 1)":1, "EBF site 362 (partition 1)":1, "EBF site 369 (partition 1)":1, "EBF site 379 (partition 1)":1, - "EBF site 384 (partition 1)":1, "EBF site 389 (partition 1)":1, - "EBF site 39 (partition 1)":1, - "EBF site 403 (partition 1)":1, - "EBF site 408 (partition 1)":1, "EBF site 417 (partition 1)":1, "EBF site 424 (partition 1)":1, - "EBF site 429 (partition 1)":1, "EBF site 431 (partition 1)":1, "EBF site 433 (partition 1)":1, - "EBF site 440 (partition 1)":1, "EBF site 441 (partition 1)":1, "EBF site 445 (partition 1)":1, "EBF site 45 (partition 1)":1, - "EBF site 454 (partition 1)":1, "EBF site 466 (partition 1)":1, "EBF site 477 (partition 1)":1, - "EBF site 478 (partition 1)":1, - "EBF site 479 (partition 1)":1, - "EBF site 481 (partition 1)":1, - "EBF site 485 (partition 1)":1, "EBF site 488 (partition 1)":1, "EBF site 489 (partition 1)":1, - "EBF site 494 (partition 1)":1, "EBF site 499 (partition 1)":1, "EBF site 50 (partition 1)":1, - "EBF site 506 (partition 1)":610.9812534626535, - "EBF site 507 (partition 1)":1, + "EBF site 506 (partition 1)":0.2258487451037979, "EBF site 509 (partition 1)":1, - "EBF site 51 (partition 1)":1, - "EBF site 513 (partition 1)":1, - "EBF site 514 (partition 1)":1, - "EBF site 515 (partition 1)":0.3749086051203841, - "EBF site 519 (partition 1)":1, + "EBF 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GTR":0.003553392842782155, - "original name":"MALLARD_VIETNAM_16_2003" + "Global MG94xREV":0.00123629096030503, + "Nucleotide GTR":0.00113802520351336 }, - "Node10":{ - "EBF site 10 (partition 1)":1, + "Node2":{ "EBF site 100 (partition 1)":1, - "EBF site 102 (partition 1)":1, + "EBF site 102 (partition 1)":0.2983773057734167, "EBF site 104 (partition 1)":1, - "EBF site 107 (partition 1)":1, - "EBF site 109 (partition 1)":1, "EBF site 11 (partition 1)":1, - "EBF site 110 (partition 1)":1, "EBF site 112 (partition 1)":1, "EBF site 113 (partition 1)":1, "EBF site 117 (partition 1)":1, @@ -2500,27 +1168,22 @@ "EBF site 136 (partition 1)":1, "EBF site 140 (partition 1)":1, "EBF site 142 (partition 1)":1, - "EBF site 145 (partition 1)":1.000000003356303, + "EBF site 145 (partition 1)":1, "EBF site 146 (partition 1)":1, - "EBF site 147 (partition 1)":1, - "EBF site 150 (partition 1)":1, "EBF site 152 (partition 1)":1, "EBF site 153 (partition 1)":1, "EBF site 154 (partition 1)":1, "EBF site 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(partition 1)":1, "EBF site 142 (partition 1)":1, - "EBF site 145 (partition 1)":159.4832746952417, + "EBF site 145 (partition 1)":1, "EBF site 146 (partition 1)":1, - "EBF site 147 (partition 1)":1, - "EBF site 150 (partition 1)":0.8001668156939907, "EBF site 152 (partition 1)":1, "EBF site 153 (partition 1)":1, - "EBF site 154 (partition 1)":39.92575073528594, + "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)":1, - "EBF site 167 (partition 1)":0.2385451274628346, - "EBF site 17 (partition 1)":1, + "EBF site 16 (partition 1)":0.9932935525732471, + "EBF site 167 (partition 1)":0.4553024703787611, "EBF site 170 (partition 1)":1, "EBF site 171 (partition 1)":1, "EBF site 172 (partition 1)":1, "EBF site 175 (partition 1)":1, - "EBF site 178 (partition 1)":0.2088079752385484, + "EBF site 178 (partition 1)":0.7349411890690492, "EBF site 181 (partition 1)":1, - "EBF site 191 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GTR":0.007656566904909031, + "Global MG94xREV":0.007944352318354534, + "Nucleotide GTR":0.00775874788653539, "original name":"SWINE_ANHUI_1_2004" } }, "attributes":{ - "EBF site 10 (partition 1)":{ - "attribute type":"branch label", - "display order":12 - }, "EBF site 100 (partition 1)":{ "attribute type":"branch label", "display order":102 @@ -5411,22 +1955,10 @@ "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 11 (partition 1)":{ "attribute type":"branch label", "display order":13 }, - "EBF site 110 (partition 1)":{ - "attribute type":"branch label", - "display order":112 - }, "EBF site 112 (partition 1)":{ "attribute type":"branch label", "display order":114 @@ -5463,14 +1995,6 @@ "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 @@ -5503,10 +2027,6 @@ "attribute type":"branch label", "display order":169 }, - "EBF site 17 (partition 1)":{ - "attribute type":"branch label", - "display order":19 - }, "EBF site 170 (partition 1)":{ "attribute type":"branch label", "display order":172 @@ -5531,14 +2051,6 @@ "attribute type":"branch label", "display order":183 }, - "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 @@ -5567,62 +2079,22 @@ "attribute type":"branch label", "display order":23 }, - "EBF site 211 (partition 1)":{ - "attribute type":"branch label", - "display order":213 - }, "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 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 @@ -5643,14 +2115,6 @@ "attribute type":"branch label", "display order":260 }, - "EBF site 265 (partition 1)":{ - "attribute type":"branch label", - "display order":267 - }, - "EBF site 271 (partition 1)":{ - "attribute type":"branch label", - "display order":273 - }, "EBF site 278 (partition 1)":{ "attribute type":"branch label", "display order":280 @@ -5663,18 +2127,10 @@ "attribute type":"branch label", "display order":30 }, - "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 298 (partition 1)":{ "attribute type":"branch label", "display order":300 @@ -5711,18 +2167,10 @@ "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 33 (partition 1)":{ - "attribute type":"branch label", - "display order":35 - }, "EBF site 332 (partition 1)":{ "attribute type":"branch label", "display order":334 @@ -5731,14 +2179,6 @@ "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 @@ -5747,10 +2187,6 @@ "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 @@ -5767,10 +2203,6 @@ "attribute type":"branch label", "display order":356 }, - "EBF site 357 (partition 1)":{ - "attribute type":"branch label", - "display order":359 - }, "EBF site 361 (partition 1)":{ "attribute type":"branch label", "display order":363 @@ -5787,26 +2219,10 @@ "attribute type":"branch label", "display order":381 }, - "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 39 (partition 1)":{ - "attribute type":"branch label", - "display order":41 - }, - "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 @@ -5815,10 +2231,6 @@ "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 @@ -5827,10 +2239,6 @@ "attribute type":"branch label", "display order":435 }, - "EBF site 440 (partition 1)":{ - "attribute type":"branch label", - "display order":442 - }, "EBF site 441 (partition 1)":{ "attribute type":"branch label", "display order":443 @@ -5843,10 +2251,6 @@ "attribute type":"branch label", "display order":47 }, - "EBF site 454 (partition 1)":{ - "attribute type":"branch label", - "display order":456 - }, "EBF site 466 (partition 1)":{ "attribute type":"branch label", "display order":468 @@ -5855,22 +2259,6 @@ "attribute type":"branch label", "display order":479 }, - "EBF site 478 (partition 1)":{ - "attribute type":"branch label", - "display order":480 - }, - "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 485 (partition 1)":{ - "attribute type":"branch label", - "display order":487 - }, "EBF site 488 (partition 1)":{ "attribute type":"branch label", "display order":490 @@ -5879,10 +2267,6 @@ "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 @@ -5895,34 +2279,14 @@ "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 @@ -5943,18 +2307,6 @@ "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 @@ -5991,22 +2343,6 @@ "attribute type":"branch label", "display order":62 }, - "EBF site 61 (partition 1)":{ - "attribute type":"branch label", - "display order":63 - }, - "EBF site 62 (partition 1)":{ - "attribute type":"branch label", - "display order":64 - }, - "EBF site 64 (partition 1)":{ - "attribute type":"branch label", - "display order":66 - }, - "EBF site 66 (partition 1)":{ - "attribute type":"branch label", - "display order":68 - }, "EBF site 68 (partition 1)":{ "attribute type":"branch label", "display order":70 @@ -6015,18 +2351,6 @@ "attribute type":"branch label", "display order":71 }, - "EBF site 70 (partition 1)":{ - "attribute type":"branch label", - "display order":72 - }, - "EBF site 73 (partition 1)":{ - "attribute type":"branch label", - "display order":75 - }, - "EBF site 77 (partition 1)":{ - "attribute type":"branch label", - "display order":79 - }, "EBF site 78 (partition 1)":{ "attribute type":"branch label", "display order":80 @@ -6039,10 +2363,6 @@ "attribute type":"branch label", "display order":10 }, - "EBF site 81 (partition 1)":{ - "attribute type":"branch label", - "display order":83 - }, "EBF site 84 (partition 1)":{ "attribute type":"branch label", "display order":86 @@ -6055,14 +2375,6 @@ "attribute type":"branch label", "display order":91 }, - "EBF site 9 (partition 1)":{ - "attribute type":"branch label", - "display order":11 - }, - "EBF site 99 (partition 1)":{ - "attribute type":"branch label", - "display order":101 - }, "Global MG94xREV":{ "attribute type":"branch length", "display order":1 @@ -6087,153 +2399,137 @@ }, "fits":{ "Global MG94xREV":{ - "AIC-c":7226.087178885974, + "AIC-c":6011.13695012892, "Equilibrium frequencies": [ -[0.0485984009412611], - [0.02956900357719973], - [0.03108082672838122], - [0.03449710399341214], - [0.02053762541952889], - [0.01249582512460089], - [0.01313471975854296], - [0.01457843439605254], - [0.02308459048229354], - [0.01404548967308914], - [0.01476361655896873], - [0.01638637286596178], - [0.03046946697462319], - [0.01853871239625653], - [0.01948657168142254], - [0.0216284558851606], - [0.02112660536120122], - [0.01285418156565452], - [0.01351139847963371], - [0.01499651610047861], - [0.008928077856285582], - [0.005432161572334556], - [0.005709900644757894], - [0.006337509553901212], - [0.01003528971321133], - [0.006105828827307119], - [0.006418011595122538], - [0.007123453161742795], - [0.01324562931848419], - [0.008059114150152886], - [0.008471165754069981], - [0.009402281622603544], - [0.03932718962871962], - [0.02392806734975356], - [0.02515147706283166], - [0.0279160244805243], - [0.01661962273972026], - [0.01011197230206122], - [0.01062898376612524], - [0.01179727815893297], - [0.01868069833194261], - [0.0113660043356041], - [0.01194713276105585], - [0.01326031269640911], - [0.02465674759639369], - [0.01500204623524711], - [0.01576908056409512], - [0.01750235335932507], - [0.02110645419006403], - [0.02462414883970813], - [0.01465982608978509], - [0.008919561995751803], - [0.009375607133978042], - [0.01040613549725428], - [0.01002571776178019], - [0.01053831914788704], - [0.0116966480569341], - [0.02174920799128454], - [0.01323299525169244], - [0.01390958039696969], - [0.01543846454447198] +[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":-3569.784907463222, + "Log Likelihood":-2978.298667783946, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *test*": [ -[0.248895715005128, 1] +[0.2932353608697501, 1] ] }, "display order":1, - "estimated parameters":43 + "estimated parameters":27 }, "Nucleotide GTR":{ - "AIC-c":7431.204675852382, + "AIC-c":6152.529196194525, "Equilibrium frequencies": [ -[0.3476574973769445], - [0.1861228958532913], - [0.2296428082660462], - [0.2365767985037179] +[0.3478363400542389], + [0.184883858035609], + [0.2307510906732697], + [0.2365287112368824] ], - "Log Likelihood":-3679.541894127126, + "Log Likelihood":-3056.215005465311, "Rate Distributions":{ - "Substitution rate from nucleotide A to nucleotide C":0.2089484190839437, + "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":0.1069376934774225, - "Substitution rate from nucleotide C to nucleotide G":0.01756475048192434, - "Substitution rate from nucleotide C to nucleotide T":1.483513244796427, - "Substitution rate from nucleotide G to nucleotide T":0.1186889750817524 + "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":36 + "estimated parameters":20 } }, "input":{ - "file name":"/tmp/tmpu23i1b/job_working_directory/000/3/working/meme_input.fa", - "number of sequences":13, + "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)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)" + "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", - "CHICKEN_HONGKONG_915_97":"test", "CK_HK_WF157_2003":"test", - "GOOSE_HONGKONG_W355_97":"test", - "GOOSE_SHANTOU_2216_2005":"test", - "HONGKONG_1_538_97":"test", - "HONGKONG_1_97_98":"test", - "HUMAN_VIETNAM_3062_2004":"test", - "HUMAN_VIETNAM_CL105_2005":"test", "MALLARD_VIETNAM_16_2003":"test", - "Node10":"test", "Node11":"test", - "Node13":"test", - "Node17":"test", - "Node18":"test", - "Node19":"test", "Node2":"test", - "Node23":"test", - "Node24":"test", - "Node25":"test", "Node3":"test", "Node4":"test", "Node5":"test", "Node7":"test", "Node9":"test", - "PEREGRINEFALCON_HK_D0028_2004":"test", "SWINE_ANHUI_1_2004":"test" } }, "timers":{ "MEME analysis":{ "order":2, - "timer":249 + "timer":437 }, "Model fitting":{ "order":1, - "timer":2 + "timer":4 }, "Total time":{ "order":0, - "timer":252 + "timer":442 } } } \ No newline at end of file