Mercurial > repos > iuc > hyphy_sm19

comparison test-data/meme-out1.json @ 0:ae7c42d49717 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:25:55 -0400
parents
children 5f1830cb9135
comparison
equal deleted inserted replaced
-1:000000000000 0:ae7c42d49717
1 {
2 "MLE":{
3 "content":{
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571 ]
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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765 "original name":"CHICKEN_CK_160_2005"
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1453 "original name":"GOOSE_HONGKONG_W355_97"
1454 },
1455 "GOOSE_SHANTOU_2216_2005":{
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1625 "original name":"GOOSE_SHANTOU_2216_2005"
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1797 "original name":"HONGKONG_1_538_97"
1798 },
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2141 "original name":"HUMAN_VIETNAM_3062_2004"
2142 },
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3000 "Node17":{
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3171 "Node18":{
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3341 },
3342 "Node19":{
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4023 "Global MG94xREV":0,
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4026 "Node25":{
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4196 },
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4365 "Global MG94xREV":0.004275976774654648,
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4367 },
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4536 "Global MG94xREV":0,
4537 "Nucleotide GTR":0.002055454494921791
4538 },
4539 "Node5":{
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4707 "Global MG94xREV":0.006421213234344543,
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4709 },
4710 "Node7":{
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4878 "Global MG94xREV":0,
4879 "Nucleotide GTR":0.003118391279351384
4880 },
4881 "Node9":{
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5387 "EBF site 84 (partition 1)":1,
5388 "EBF site 86 (partition 1)":1,
5389 "EBF site 89 (partition 1)":1,
5390 "EBF site 9 (partition 1)":1,
5391 "EBF site 99 (partition 1)":0.8274022600721103,
5392 "Global MG94xREV":0.01081751233170446,
5393 "Nucleotide GTR":0.007656566904909031,
5394 "original name":"SWINE_ANHUI_1_2004"
5395 }
5396 },
5397 "attributes":{
5398 "EBF site 10 (partition 1)":{
5399 "attribute type":"branch label",
5400 "display order":12
5401 },
5402 "EBF site 100 (partition 1)":{
5403 "attribute type":"branch label",
5404 "display order":102
5405 },
5406 "EBF site 102 (partition 1)":{
5407 "attribute type":"branch label",
5408 "display order":104
5409 },
5410 "EBF site 104 (partition 1)":{
5411 "attribute type":"branch label",
5412 "display order":106
5413 },
5414 "EBF site 107 (partition 1)":{
5415 "attribute type":"branch label",
5416 "display order":109
5417 },
5418 "EBF site 109 (partition 1)":{
5419 "attribute type":"branch label",
5420 "display order":111
5421 },
5422 "EBF site 11 (partition 1)":{
5423 "attribute type":"branch label",
5424 "display order":13
5425 },
5426 "EBF site 110 (partition 1)":{
5427 "attribute type":"branch label",
5428 "display order":112
5429 },
5430 "EBF site 112 (partition 1)":{
5431 "attribute type":"branch label",
5432 "display order":114
5433 },
5434 "EBF site 113 (partition 1)":{
5435 "attribute type":"branch label",
5436 "display order":115
5437 },
5438 "EBF site 117 (partition 1)":{
5439 "attribute type":"branch label",
5440 "display order":119
5441 },
5442 "EBF site 12 (partition 1)":{
5443 "attribute type":"branch label",
5444 "display order":14
5445 },
5446 "EBF site 136 (partition 1)":{
5447 "attribute type":"branch label",
5448 "display order":138
5449 },
5450 "EBF site 140 (partition 1)":{
5451 "attribute type":"branch label",
5452 "display order":142
5453 },
5454 "EBF site 142 (partition 1)":{
5455 "attribute type":"branch label",
5456 "display order":144
5457 },
5458 "EBF site 145 (partition 1)":{
5459 "attribute type":"branch label",
5460 "display order":147
5461 },
5462 "EBF site 146 (partition 1)":{
5463 "attribute type":"branch label",
5464 "display order":148
5465 },
5466 "EBF site 147 (partition 1)":{
5467 "attribute type":"branch label",
5468 "display order":149
5469 },
5470 "EBF site 150 (partition 1)":{
5471 "attribute type":"branch label",
5472 "display order":152
5473 },
5474 "EBF site 152 (partition 1)":{
5475 "attribute type":"branch label",
5476 "display order":154
5477 },
5478 "EBF site 153 (partition 1)":{
5479 "attribute type":"branch label",
5480 "display order":155
5481 },
5482 "EBF site 154 (partition 1)":{
5483 "attribute type":"branch label",
5484 "display order":156
5485 },
5486 "EBF site 155 (partition 1)":{
5487 "attribute type":"branch label",
5488 "display order":157
5489 },
5490 "EBF site 156 (partition 1)":{
5491 "attribute type":"branch label",
5492 "display order":158
5493 },
5494 "EBF site 157 (partition 1)":{
5495 "attribute type":"branch label",
5496 "display order":159
5497 },
5498 "EBF site 16 (partition 1)":{
5499 "attribute type":"branch label",
5500 "display order":18
5501 },
5502 "EBF site 167 (partition 1)":{
5503 "attribute type":"branch label",
5504 "display order":169
5505 },
5506 "EBF site 17 (partition 1)":{
5507 "attribute type":"branch label",
5508 "display order":19
5509 },
5510 "EBF site 170 (partition 1)":{
5511 "attribute type":"branch label",
5512 "display order":172
5513 },
5514 "EBF site 171 (partition 1)":{
5515 "attribute type":"branch label",
5516 "display order":173
5517 },
5518 "EBF site 172 (partition 1)":{
5519 "attribute type":"branch label",
5520 "display order":174
5521 },
5522 "EBF site 175 (partition 1)":{
5523 "attribute type":"branch label",
5524 "display order":177
5525 },
5526 "EBF site 178 (partition 1)":{
5527 "attribute type":"branch label",
5528 "display order":180
5529 },
5530 "EBF site 181 (partition 1)":{
5531 "attribute type":"branch label",
5532 "display order":183
5533 },
5534 "EBF site 191 (partition 1)":{
5535 "attribute type":"branch label",
5536 "display order":193
5537 },
5538 "EBF site 195 (partition 1)":{
5539 "attribute type":"branch label",
5540 "display order":197
5541 },
5542 "EBF site 196 (partition 1)":{
5543 "attribute type":"branch label",
5544 "display order":198
5545 },
5546 "EBF site 197 (partition 1)":{
5547 "attribute type":"branch label",
5548 "display order":199
5549 },
5550 "EBF site 200 (partition 1)":{
5551 "attribute type":"branch label",
5552 "display order":202
5553 },
5554 "EBF site 204 (partition 1)":{
5555 "attribute type":"branch label",
5556 "display order":206
5557 },
5558 "EBF site 206 (partition 1)":{
5559 "attribute type":"branch label",
5560 "display order":208
5561 },
5562 "EBF site 209 (partition 1)":{
5563 "attribute type":"branch label",
5564 "display order":211
5565 },
5566 "EBF site 21 (partition 1)":{
5567 "attribute type":"branch label",
5568 "display order":23
5569 },
5570 "EBF site 211 (partition 1)":{
5571 "attribute type":"branch label",
5572 "display order":213
5573 },
5574 "EBF site 213 (partition 1)":{
5575 "attribute type":"branch label",
5576 "display order":215
5577 },
5578 "EBF site 214 (partition 1)":{
5579 "attribute type":"branch label",
5580 "display order":216
5581 },
5582 "EBF site 217 (partition 1)":{
5583 "attribute type":"branch label",
5584 "display order":219
5585 },
5586 "EBF site 221 (partition 1)":{
5587 "attribute type":"branch label",
5588 "display order":223
5589 },
5590 "EBF site 222 (partition 1)":{
5591 "attribute type":"branch label",
5592 "display order":224
5593 },
5594 "EBF site 224 (partition 1)":{
5595 "attribute type":"branch label",
5596 "display order":226
5597 },
5598 "EBF site 226 (partition 1)":{
5599 "attribute type":"branch label",
5600 "display order":228
5601 },
5602 "EBF site 228 (partition 1)":{
5603 "attribute type":"branch label",
5604 "display order":230
5605 },
5606 "EBF site 230 (partition 1)":{
5607 "attribute type":"branch label",
5608 "display order":232
5609 },
5610 "EBF site 231 (partition 1)":{
5611 "attribute type":"branch label",
5612 "display order":233
5613 },
5614 "EBF site 233 (partition 1)":{
5615 "attribute type":"branch label",
5616 "display order":235
5617 },
5618 "EBF site 237 (partition 1)":{
5619 "attribute type":"branch label",
5620 "display order":239
5621 },
5622 "EBF site 240 (partition 1)":{
5623 "attribute type":"branch label",
5624 "display order":242
5625 },
5626 "EBF site 241 (partition 1)":{
5627 "attribute type":"branch label",
5628 "display order":243
5629 },
5630 "EBF site 250 (partition 1)":{
5631 "attribute type":"branch label",
5632 "display order":252
5633 },
5634 "EBF site 254 (partition 1)":{
5635 "attribute type":"branch label",
5636 "display order":256
5637 },
5638 "EBF site 256 (partition 1)":{
5639 "attribute type":"branch label",
5640 "display order":258
5641 },
5642 "EBF site 258 (partition 1)":{
5643 "attribute type":"branch label",
5644 "display order":260
5645 },
5646 "EBF site 265 (partition 1)":{
5647 "attribute type":"branch label",
5648 "display order":267
5649 },
5650 "EBF site 271 (partition 1)":{
5651 "attribute type":"branch label",
5652 "display order":273
5653 },
5654 "EBF site 278 (partition 1)":{
5655 "attribute type":"branch label",
5656 "display order":280
5657 },
5658 "EBF site 279 (partition 1)":{
5659 "attribute type":"branch label",
5660 "display order":281
5661 },
5662 "EBF site 28 (partition 1)":{
5663 "attribute type":"branch label",
5664 "display order":30
5665 },
5666 "EBF site 283 (partition 1)":{
5667 "attribute type":"branch label",
5668 "display order":285
5669 },
5670 "EBF site 288 (partition 1)":{
5671 "attribute type":"branch label",
5672 "display order":290
5673 },
5674 "EBF site 291 (partition 1)":{
5675 "attribute type":"branch label",
5676 "display order":293
5677 },
5678 "EBF site 298 (partition 1)":{
5679 "attribute type":"branch label",
5680 "display order":300
5681 },
5682 "EBF site 3 (partition 1)":{
5683 "attribute type":"branch label",
5684 "display order":5
5685 },
5686 "EBF site 302 (partition 1)":{
5687 "attribute type":"branch label",
5688 "display order":304
5689 },
5690 "EBF site 304 (partition 1)":{
5691 "attribute type":"branch label",
5692 "display order":306
5693 },
5694 "EBF site 306 (partition 1)":{
5695 "attribute type":"branch label",
5696 "display order":308
5697 },
5698 "EBF site 309 (partition 1)":{
5699 "attribute type":"branch label",
5700 "display order":311
5701 },
5702 "EBF site 312 (partition 1)":{
5703 "attribute type":"branch label",
5704 "display order":314
5705 },
5706 "EBF site 315 (partition 1)":{
5707 "attribute type":"branch label",
5708 "display order":317
5709 },
5710 "EBF site 327 (partition 1)":{
5711 "attribute type":"branch label",
5712 "display order":329
5713 },
5714 "EBF site 328 (partition 1)":{
5715 "attribute type":"branch label",
5716 "display order":330
5717 },
5718 "EBF site 329 (partition 1)":{
5719 "attribute type":"branch label",
5720 "display order":331
5721 },
5722 "EBF site 33 (partition 1)":{
5723 "attribute type":"branch label",
5724 "display order":35
5725 },
5726 "EBF site 332 (partition 1)":{
5727 "attribute type":"branch label",
5728 "display order":334
5729 },
5730 "EBF site 336 (partition 1)":{
5731 "attribute type":"branch label",
5732 "display order":338
5733 },
5734 "EBF site 338 (partition 1)":{
5735 "attribute type":"branch label",
5736 "display order":340
5737 },
5738 "EBF site 339 (partition 1)":{
5739 "attribute type":"branch label",
5740 "display order":341
5741 },
5742 "EBF site 341 (partition 1)":{
5743 "attribute type":"branch label",
5744 "display order":343
5745 },
5746 "EBF site 342 (partition 1)":{
5747 "attribute type":"branch label",
5748 "display order":344
5749 },
5750 "EBF site 344 (partition 1)":{
5751 "attribute type":"branch label",
5752 "display order":346
5753 },
5754 "EBF site 348 (partition 1)":{
5755 "attribute type":"branch label",
5756 "display order":350
5757 },
5758 "EBF site 351 (partition 1)":{
5759 "attribute type":"branch label",
5760 "display order":353
5761 },
5762 "EBF site 353 (partition 1)":{
5763 "attribute type":"branch label",
5764 "display order":355
5765 },
5766 "EBF site 354 (partition 1)":{
5767 "attribute type":"branch label",
5768 "display order":356
5769 },
5770 "EBF site 357 (partition 1)":{
5771 "attribute type":"branch label",
5772 "display order":359
5773 },
5774 "EBF site 361 (partition 1)":{
5775 "attribute type":"branch label",
5776 "display order":363
5777 },
5778 "EBF site 362 (partition 1)":{
5779 "attribute type":"branch label",
5780 "display order":364
5781 },
5782 "EBF site 369 (partition 1)":{
5783 "attribute type":"branch label",
5784 "display order":371
5785 },
5786 "EBF site 379 (partition 1)":{
5787 "attribute type":"branch label",
5788 "display order":381
5789 },
5790 "EBF site 384 (partition 1)":{
5791 "attribute type":"branch label",
5792 "display order":386
5793 },
5794 "EBF site 389 (partition 1)":{
5795 "attribute type":"branch label",
5796 "display order":391
5797 },
5798 "EBF site 39 (partition 1)":{
5799 "attribute type":"branch label",
5800 "display order":41
5801 },
5802 "EBF site 403 (partition 1)":{
5803 "attribute type":"branch label",
5804 "display order":405
5805 },
5806 "EBF site 408 (partition 1)":{
5807 "attribute type":"branch label",
5808 "display order":410
5809 },
5810 "EBF site 417 (partition 1)":{
5811 "attribute type":"branch label",
5812 "display order":419
5813 },
5814 "EBF site 424 (partition 1)":{
5815 "attribute type":"branch label",
5816 "display order":426
5817 },
5818 "EBF site 429 (partition 1)":{
5819 "attribute type":"branch label",
5820 "display order":431
5821 },
5822 "EBF site 431 (partition 1)":{
5823 "attribute type":"branch label",
5824 "display order":433
5825 },
5826 "EBF site 433 (partition 1)":{
5827 "attribute type":"branch label",
5828 "display order":435
5829 },
5830 "EBF site 440 (partition 1)":{
5831 "attribute type":"branch label",
5832 "display order":442
5833 },
5834 "EBF site 441 (partition 1)":{
5835 "attribute type":"branch label",
5836 "display order":443
5837 },
5838 "EBF site 445 (partition 1)":{
5839 "attribute type":"branch label",
5840 "display order":447
5841 },
5842 "EBF site 45 (partition 1)":{
5843 "attribute type":"branch label",
5844 "display order":47
5845 },
5846 "EBF site 454 (partition 1)":{
5847 "attribute type":"branch label",
5848 "display order":456
5849 },
5850 "EBF site 466 (partition 1)":{
5851 "attribute type":"branch label",
5852 "display order":468
5853 },
5854 "EBF site 477 (partition 1)":{
5855 "attribute type":"branch label",
5856 "display order":479
5857 },
5858 "EBF site 478 (partition 1)":{
5859 "attribute type":"branch label",
5860 "display order":480
5861 },
5862 "EBF site 479 (partition 1)":{
5863 "attribute type":"branch label",
5864 "display order":481
5865 },
5866 "EBF site 481 (partition 1)":{
5867 "attribute type":"branch label",
5868 "display order":483
5869 },
5870 "EBF site 485 (partition 1)":{
5871 "attribute type":"branch label",
5872 "display order":487
5873 },
5874 "EBF site 488 (partition 1)":{
5875 "attribute type":"branch label",
5876 "display order":490
5877 },
5878 "EBF site 489 (partition 1)":{
5879 "attribute type":"branch label",
5880 "display order":491
5881 },
5882 "EBF site 494 (partition 1)":{
5883 "attribute type":"branch label",
5884 "display order":496
5885 },
5886 "EBF site 499 (partition 1)":{
5887 "attribute type":"branch label",
5888 "display order":501
5889 },
5890 "EBF site 50 (partition 1)":{
5891 "attribute type":"branch label",
5892 "display order":52
5893 },
5894 "EBF site 506 (partition 1)":{
5895 "attribute type":"branch label",
5896 "display order":508
5897 },
5898 "EBF site 507 (partition 1)":{
5899 "attribute type":"branch label",
5900 "display order":509
5901 },
5902 "EBF site 509 (partition 1)":{
5903 "attribute type":"branch label",
5904 "display order":511
5905 },
5906 "EBF site 51 (partition 1)":{
5907 "attribute type":"branch label",
5908 "display order":53
5909 },
5910 "EBF site 513 (partition 1)":{
5911 "attribute type":"branch label",
5912 "display order":515
5913 },
5914 "EBF site 514 (partition 1)":{
5915 "attribute type":"branch label",
5916 "display order":516
5917 },
5918 "EBF site 515 (partition 1)":{
5919 "attribute type":"branch label",
5920 "display order":517
5921 },
5922 "EBF site 519 (partition 1)":{
5923 "attribute type":"branch label",
5924 "display order":521
5925 },
5926 "EBF site 52 (partition 1)":{
5927 "attribute type":"branch label",
5928 "display order":54
5929 },
5930 "EBF site 527 (partition 1)":{
5931 "attribute type":"branch label",
5932 "display order":529
5933 },
5934 "EBF site 529 (partition 1)":{
5935 "attribute type":"branch label",
5936 "display order":531
5937 },
5938 "EBF site 537 (partition 1)":{
5939 "attribute type":"branch label",
5940 "display order":539
5941 },
5942 "EBF site 539 (partition 1)":{
5943 "attribute type":"branch label",
5944 "display order":541
5945 },
5946 "EBF site 54 (partition 1)":{
5947 "attribute type":"branch label",
5948 "display order":56
5949 },
5950 "EBF site 540 (partition 1)":{
5951 "attribute type":"branch label",
5952 "display order":542
5953 },
5954 "EBF site 544 (partition 1)":{
5955 "attribute type":"branch label",
5956 "display order":546
5957 },
5958 "EBF site 545 (partition 1)":{
5959 "attribute type":"branch label",
5960 "display order":547
5961 },
5962 "EBF site 549 (partition 1)":{
5963 "attribute type":"branch label",
5964 "display order":551
5965 },
5966 "EBF site 553 (partition 1)":{
5967 "attribute type":"branch label",
5968 "display order":555
5969 },
5970 "EBF site 558 (partition 1)":{
5971 "attribute type":"branch label",
5972 "display order":560
5973 },
5974 "EBF site 560 (partition 1)":{
5975 "attribute type":"branch label",
5976 "display order":562
5977 },
5978 "EBF site 564 (partition 1)":{
5979 "attribute type":"branch label",
5980 "display order":566
5981 },
5982 "EBF site 58 (partition 1)":{
5983 "attribute type":"branch label",
5984 "display order":60
5985 },
5986 "EBF site 59 (partition 1)":{
5987 "attribute type":"branch label",
5988 "display order":61
5989 },
5990 "EBF site 60 (partition 1)":{
5991 "attribute type":"branch label",
5992 "display order":62
5993 },
5994 "EBF site 61 (partition 1)":{
5995 "attribute type":"branch label",
5996 "display order":63
5997 },
5998 "EBF site 62 (partition 1)":{
5999 "attribute type":"branch label",
6000 "display order":64
6001 },
6002 "EBF site 64 (partition 1)":{
6003 "attribute type":"branch label",
6004 "display order":66
6005 },
6006 "EBF site 66 (partition 1)":{
6007 "attribute type":"branch label",
6008 "display order":68
6009 },
6010 "EBF site 68 (partition 1)":{
6011 "attribute type":"branch label",
6012 "display order":70
6013 },
6014 "EBF site 69 (partition 1)":{
6015 "attribute type":"branch label",
6016 "display order":71
6017 },
6018 "EBF site 70 (partition 1)":{
6019 "attribute type":"branch label",
6020 "display order":72
6021 },
6022 "EBF site 73 (partition 1)":{
6023 "attribute type":"branch label",
6024 "display order":75
6025 },
6026 "EBF site 77 (partition 1)":{
6027 "attribute type":"branch label",
6028 "display order":79
6029 },
6030 "EBF site 78 (partition 1)":{
6031 "attribute type":"branch label",
6032 "display order":80
6033 },
6034 "EBF site 79 (partition 1)":{
6035 "attribute type":"branch label",
6036 "display order":81
6037 },
6038 "EBF site 8 (partition 1)":{
6039 "attribute type":"branch label",
6040 "display order":10
6041 },
6042 "EBF site 81 (partition 1)":{
6043 "attribute type":"branch label",
6044 "display order":83
6045 },
6046 "EBF site 84 (partition 1)":{
6047 "attribute type":"branch label",
6048 "display order":86
6049 },
6050 "EBF site 86 (partition 1)":{
6051 "attribute type":"branch label",
6052 "display order":88
6053 },
6054 "EBF site 89 (partition 1)":{
6055 "attribute type":"branch label",
6056 "display order":91
6057 },
6058 "EBF site 9 (partition 1)":{
6059 "attribute type":"branch label",
6060 "display order":11
6061 },
6062 "EBF site 99 (partition 1)":{
6063 "attribute type":"branch label",
6064 "display order":101
6065 },
6066 "Global MG94xREV":{
6067 "attribute type":"branch length",
6068 "display order":1
6069 },
6070 "Nucleotide GTR":{
6071 "attribute type":"branch length",
6072 "display order":0
6073 },
6074 "original name":{
6075 "attribute type":"node label",
6076 "display order":-1
6077 }
6078 }
6079 },
6080 "data partitions":{
6081 "0":{
6082 "coverage": [
6083 [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]
6084 ],
6085 "name":"meme.filter.default"
6086 }
6087 },
6088 "fits":{
6089 "Global MG94xREV":{
6090 "AIC-c":7226.087178885974,
6091 "Equilibrium frequencies": [
6092 [0.0485984009412611],
6093 [0.02956900357719973],
6094 [0.03108082672838122],
6095 [0.03449710399341214],
6096 [0.02053762541952889],
6097 [0.01249582512460089],
6098 [0.01313471975854296],
6099 [0.01457843439605254],
6100 [0.02308459048229354],
6101 [0.01404548967308914],
6102 [0.01476361655896873],
6103 [0.01638637286596178],
6104 [0.03046946697462319],
6105 [0.01853871239625653],
6106 [0.01948657168142254],
6107 [0.0216284558851606],
6108 [0.02112660536120122],
6109 [0.01285418156565452],
6110 [0.01351139847963371],
6111 [0.01499651610047861],
6112 [0.008928077856285582],
6113 [0.005432161572334556],
6114 [0.005709900644757894],
6115 [0.006337509553901212],
6116 [0.01003528971321133],
6117 [0.006105828827307119],
6118 [0.006418011595122538],
6119 [0.007123453161742795],
6120 [0.01324562931848419],
6121 [0.008059114150152886],
6122 [0.008471165754069981],
6123 [0.009402281622603544],
6124 [0.03932718962871962],
6125 [0.02392806734975356],
6126 [0.02515147706283166],
6127 [0.0279160244805243],
6128 [0.01661962273972026],
6129 [0.01011197230206122],
6130 [0.01062898376612524],
6131 [0.01179727815893297],
6132 [0.01868069833194261],
6133 [0.0113660043356041],
6134 [0.01194713276105585],
6135 [0.01326031269640911],
6136 [0.02465674759639369],
6137 [0.01500204623524711],
6138 [0.01576908056409512],
6139 [0.01750235335932507],
6140 [0.02110645419006403],
6141 [0.02462414883970813],
6142 [0.01465982608978509],
6143 [0.008919561995751803],
6144 [0.009375607133978042],
6145 [0.01040613549725428],
6146 [0.01002571776178019],
6147 [0.01053831914788704],
6148 [0.0116966480569341],
6149 [0.02174920799128454],
6150 [0.01323299525169244],
6151 [0.01390958039696969],
6152 [0.01543846454447198]
6153 ],
6154 "Log Likelihood":-3569.784907463222,
6155 "Rate Distributions":{
6156 "non-synonymous/synonymous rate ratio for *test*": [
6157 [0.248895715005128, 1]
6158 ]
6159 },
6160 "display order":1,
6161 "estimated parameters":43
6162 },
6163 "Nucleotide GTR":{
6164 "AIC-c":7431.204675852382,
6165 "Equilibrium frequencies": [
6166 [0.3476574973769445],
6167 [0.1861228958532913],
6168 [0.2296428082660462],
6169 [0.2365767985037179]
6170 ],
6171 "Log Likelihood":-3679.541894127126,
6172 "Rate Distributions":{
6173 "Substitution rate from nucleotide A to nucleotide C":0.2089484190839437,
6174 "Substitution rate from nucleotide A to nucleotide G":1,
6175 "Substitution rate from nucleotide A to nucleotide T":0.1069376934774225,
6176 "Substitution rate from nucleotide C to nucleotide G":0.01756475048192434,
6177 "Substitution rate from nucleotide C to nucleotide T":1.483513244796427,
6178 "Substitution rate from nucleotide G to nucleotide T":0.1186889750817524
6179 },
6180 "display order":0,
6181 "estimated parameters":36
6182 }
6183 },
6184 "input":{
6185 "file name":"/tmp/tmpu23i1b/job_working_directory/000/3/working/meme_input.fa",
6186 "number of sequences":13,
6187 "number of sites":566,
6188 "partition count":1,
6189 "trees":{
6190 "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)"
6191 }
6192 },
6193 "tested":{
6194 "0":{
6195 "CHICKEN_CK_160_2005":"test",
6196 "CHICKEN_HEBEI_326_2005":"test",
6197 "CHICKEN_HONGKONG_915_97":"test",
6198 "CK_HK_WF157_2003":"test",
6199 "GOOSE_HONGKONG_W355_97":"test",
6200 "GOOSE_SHANTOU_2216_2005":"test",
6201 "HONGKONG_1_538_97":"test",
6202 "HONGKONG_1_97_98":"test",
6203 "HUMAN_VIETNAM_3062_2004":"test",
6204 "HUMAN_VIETNAM_CL105_2005":"test",
6205 "MALLARD_VIETNAM_16_2003":"test",
6206 "Node10":"test",
6207 "Node11":"test",
6208 "Node13":"test",
6209 "Node17":"test",
6210 "Node18":"test",
6211 "Node19":"test",
6212 "Node2":"test",
6213 "Node23":"test",
6214 "Node24":"test",
6215 "Node25":"test",
6216 "Node3":"test",
6217 "Node4":"test",
6218 "Node5":"test",
6219 "Node7":"test",
6220 "Node9":"test",
6221 "PEREGRINEFALCON_HK_D0028_2004":"test",
6222 "SWINE_ANHUI_1_2004":"test"
6223 }
6224 },
6225 "timers":{
6226 "MEME analysis":{
6227 "order":2,
6228 "timer":249
6229 },
6230 "Model fitting":{
6231 "order":1,
6232 "timer":2
6233 },
6234 "Total time":{
6235 "order":0,
6236 "timer":252
6237 }
6238 }
6239 }