bio-phyloxml 0.9.0
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- data/.document +5 -0
- data/.travis.yml +12 -0
- data/Gemfile +13 -0
- data/LICENSE.txt +20 -0
- data/README.md +199 -0
- data/README.rdoc +48 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/lib/bio-phyloxml.rb +12 -0
- data/lib/bio/phyloxml.rb +3 -0
- data/lib/bio/phyloxml/elements.rb +1166 -0
- data/lib/bio/phyloxml/parser.rb +1000 -0
- data/lib/bio/phyloxml/phyloxml.xsd +582 -0
- data/lib/bio/phyloxml/writer.rb +227 -0
- data/sample/test_phyloxml_big.rb +205 -0
- data/test/data/phyloxml/apaf.xml +666 -0
- data/test/data/phyloxml/bcl_2.xml +2097 -0
- data/test/data/phyloxml/made_up.xml +144 -0
- data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
- data/test/data/phyloxml/phyloxml_examples.xml +415 -0
- data/test/helper.rb +25 -0
- data/test/unit/bio/test_phyloxml.rb +821 -0
- data/test/unit/bio/test_phyloxml_writer.rb +334 -0
- metadata +155 -0
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318
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319
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320
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321
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322
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323
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<code>BRARE</code>
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|
324
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|
325
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+
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|
326
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+
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327
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+
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|
328
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+
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|
329
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+
<taxonomy>
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|
330
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<code>BRARE</code>
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|
331
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+
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|
332
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+
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|
333
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+
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334
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+
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|
335
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+
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|
336
|
+
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|
337
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+
<taxonomy>
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|
338
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+
<code>TETNG</code>
|
|
339
|
+
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|
340
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+
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341
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+
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|
342
|
+
<clade>
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|
343
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+
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|
344
|
+
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|
345
|
+
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|
346
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+
<speciations>1</speciations>
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|
347
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+
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|
348
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+
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|
349
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+
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|
350
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|
351
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+
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352
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353
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354
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355
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<name>122_MOUSE</name>
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|
356
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357
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|
358
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<code>MOUSE</code>
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|
359
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360
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361
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<clade>
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362
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|
363
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+
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|
364
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+
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365
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<speciations>1</speciations>
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366
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367
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|
368
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|
369
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+
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|
370
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371
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+
<duplications>1</duplications>
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372
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</events>
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373
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<clade>
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374
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|
375
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+
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376
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+
<events>
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377
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<speciations>1</speciations>
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378
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379
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380
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|
381
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382
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<taxonomy>
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|
383
|
+
<code>HUMAN</code>
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|
384
|
+
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|
385
|
+
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|
386
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<clade>
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|
387
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|
388
|
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|
389
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<taxonomy>
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|
390
|
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<code>BOVIN</code>
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|
391
|
+
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|
392
|
+
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|
393
|
+
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|
394
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|
395
|
+
<name>92_CANFA</name>
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|
396
|
+
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|
397
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+
<taxonomy>
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|
398
|
+
<code>CANFA</code>
|
|
399
|
+
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|
400
|
+
</clade>
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|
401
|
+
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|
402
|
+
<clade>
|
|
403
|
+
<name>46_CHICK</name>
|
|
404
|
+
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|
405
|
+
<taxonomy>
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|
406
|
+
<code>CHICK</code>
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|
407
|
+
</taxonomy>
|
|
408
|
+
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|
409
|
+
</clade>
|
|
410
|
+
</clade>
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|
411
|
+
<clade>
|
|
412
|
+
<name>147_XENLA</name>
|
|
413
|
+
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|
|
414
|
+
<taxonomy>
|
|
415
|
+
<code>XENLA</code>
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|
416
|
+
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|
417
|
+
</clade>
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|
418
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</clade>
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|
419
|
+
</clade>
|
|
420
|
+
</clade>
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|
421
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+
</clade>
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|
422
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<clade>
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|
423
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<branch_length>0.21984499999999996</branch_length>
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|
424
|
+
<confidence type="bootstrap">33.0</confidence>
|
|
425
|
+
<events>
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|
426
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+
<duplications>1</duplications>
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|
427
|
+
</events>
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|
428
|
+
<clade>
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|
429
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|
|
430
|
+
<confidence type="bootstrap">14.0</confidence>
|
|
431
|
+
<events>
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|
432
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+
<duplications>1</duplications>
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|
433
|
+
</events>
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|
434
|
+
<clade>
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|
435
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+
<branch_length>0.07066</branch_length>
|
|
436
|
+
<confidence type="bootstrap">2.0</confidence>
|
|
437
|
+
<events>
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|
438
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+
<duplications>1</duplications>
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|
439
|
+
</events>
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|
440
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+
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|
441
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|
442
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+
<confidence type="bootstrap">3.0</confidence>
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|
443
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+
<events>
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444
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<speciations>1</speciations>
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445
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+
</events>
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446
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447
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448
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<confidence type="bootstrap">4.0</confidence>
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|
449
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+
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|
450
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<duplications>1</duplications>
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451
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452
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453
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454
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<confidence type="bootstrap">15.0</confidence>
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455
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456
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<speciations>1</speciations>
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457
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458
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459
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|
460
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461
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462
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<speciations>1</speciations>
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463
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464
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|
465
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|
466
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<confidence type="bootstrap">52.0</confidence>
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|
467
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+
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|
468
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<duplications>1</duplications>
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|
469
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+
</events>
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|
470
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<clade>
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|
471
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|
472
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<confidence type="bootstrap">76.0</confidence>
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473
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+
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474
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<duplications>1</duplications>
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475
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+
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476
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|
477
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|
478
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<confidence type="bootstrap">55.0</confidence>
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|
479
|
+
<events>
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|
480
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<speciations>1</speciations>
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|
481
|
+
</events>
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|
482
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<clade>
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|
483
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<name>140_TETNG</name>
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|
484
|
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485
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<taxonomy>
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|
486
|
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<code>TETNG</code>
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487
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488
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489
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<clade>
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|
490
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|
491
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<confidence type="bootstrap">43.0</confidence>
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492
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493
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<speciations>1</speciations>
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494
|
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495
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496
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<name>152_XENLA</name>
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|
497
|
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498
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<taxonomy>
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|
499
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<code>XENLA</code>
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|
500
|
+
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501
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|
502
|
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<clade>
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|
503
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504
|
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<confidence type="bootstrap">35.0</confidence>
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505
|
+
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506
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<speciations>1</speciations>
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507
|
+
</events>
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|
508
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+
<clade>
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|
509
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<branch_length>0.06125</branch_length>
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|
510
|
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<confidence type="bootstrap">68.0</confidence>
|
|
511
|
+
<events>
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|
512
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<duplications>1</duplications>
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|
513
|
+
</events>
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|
514
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<clade>
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|
515
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<branch_length>1.0E-5</branch_length>
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|
516
|
+
<confidence type="bootstrap">93.0</confidence>
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|
517
|
+
<events>
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|
518
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<duplications>1</duplications>
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|
519
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</events>
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520
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<clade>
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|
521
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<branch_length>1.0E-5</branch_length>
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|
522
|
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<confidence type="bootstrap">75.0</confidence>
|
|
523
|
+
<events>
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|
524
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<speciations>1</speciations>
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|
525
|
+
</events>
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|
526
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|
527
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<name>0_HUMAN</name>
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|
528
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529
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<taxonomy>
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|
530
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<code>HUMAN</code>
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|
531
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|
532
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|
533
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<clade>
|
|
534
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<name>72_BOVIN</name>
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|
535
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536
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<taxonomy>
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|
537
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<code>BOVIN</code>
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|
538
|
+
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|
539
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|
540
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</clade>
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|
541
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<clade>
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|
542
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<name>123_MOUSE</name>
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|
543
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544
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<taxonomy>
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|
545
|
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<code>MOUSE</code>
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|
546
|
+
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|
547
|
+
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|
548
|
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|
549
|
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|
550
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<name>97_CANFA</name>
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|
551
|
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552
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<taxonomy>
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|
553
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<code>CANFA</code>
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|
554
|
+
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|
555
|
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|
556
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|
557
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|
558
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559
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560
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<taxonomy>
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561
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<code>CHICK</code>
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562
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563
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|
564
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|
565
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|
566
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567
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568
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569
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570
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571
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<speciations>1</speciations>
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572
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573
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574
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575
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576
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+
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577
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<speciations>1</speciations>
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578
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|
579
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580
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|
581
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|
582
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|
583
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<duplications>1</duplications>
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|
584
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585
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586
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|
587
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588
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<taxonomy>
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589
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<code>TETNG</code>
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590
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591
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592
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593
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|
594
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595
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596
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<code>TETNG</code>
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597
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598
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|
599
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|
600
|
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|
601
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|
602
|
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603
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|
604
|
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<code>FUGRU</code>
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|
605
|
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606
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607
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|
608
|
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|
609
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610
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611
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|
612
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<code>BRARE</code>
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613
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614
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615
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616
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617
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618
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619
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620
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621
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622
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623
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624
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625
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626
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627
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<speciations>1</speciations>
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628
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629
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630
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631
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632
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633
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<code>XENLA</code>
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634
|
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635
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636
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637
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638
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<confidence type="bootstrap">100.0</confidence>
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639
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640
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<duplications>1</duplications>
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641
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642
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643
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<name>126_MOUSE</name>
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|
644
|
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645
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<taxonomy>
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|
646
|
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<code>MOUSE</code>
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|
647
|
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648
|
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649
|
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|
650
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651
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<confidence type="bootstrap">100.0</confidence>
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|
652
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653
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<duplications>1</duplications>
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|
654
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655
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658
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714
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719
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720
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721
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734
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735
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736
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737
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741
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742
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747
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748
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749
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763
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769
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814
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815
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820
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821
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822
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827
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828
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829
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830
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831
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832
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833
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834
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835
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836
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840
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841
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842
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843
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844
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847
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848
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850
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851
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852
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853
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854
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855
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856
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857
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858
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860
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861
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863
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864
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866
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867
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868
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869
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870
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871
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873
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874
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875
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876
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877
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879
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880
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881
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882
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883
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884
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885
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886
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887
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888
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889
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890
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891
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892
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893
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894
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895
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896
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897
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898
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900
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901
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902
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904
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906
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907
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908
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909
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910
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911
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912
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913
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914
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915
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916
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917
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919
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920
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921
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922
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923
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924
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926
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927
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928
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929
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930
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932
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933
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934
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935
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936
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937
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938
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939
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940
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941
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942
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943
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944
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946
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947
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948
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949
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950
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951
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952
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953
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954
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955
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956
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958
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959
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960
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962
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963
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964
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965
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967
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969
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970
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971
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972
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973
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974
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975
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976
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977
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978
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979
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980
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981
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<code>SPHGR</code>
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982
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983
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985
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986
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987
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988
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989
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|
990
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991
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1000
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1001
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1002
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1003
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1005
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1007
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1008
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1009
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1010
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1022
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1026
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1028
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1029
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1030
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1032
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1034
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1035
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1036
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1039
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1040
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1045
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1046
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1047
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1048
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1053
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1054
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1055
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1057
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1060
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1061
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1062
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1066
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1067
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1068
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1069
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1070
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1072
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1074
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1075
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1076
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1077
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1078
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1079
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1080
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1081
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1082
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1083
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1084
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1085
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1087
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1088
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1089
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1090
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1094
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1095
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1096
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1097
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1098
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1100
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1101
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1102
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1103
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<confidence type="bootstrap">100.0</confidence>
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1104
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1105
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<duplications>1</duplications>
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1106
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1107
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1108
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1109
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1110
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1111
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<code>BOVIN</code>
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1112
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1113
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1114
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1115
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1116
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1117
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1118
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1119
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1120
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1121
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1122
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1123
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1124
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1125
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1126
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1127
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1128
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1129
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1130
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1131
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1132
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1133
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1134
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1135
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1136
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1137
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1138
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1139
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1140
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1141
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1142
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1143
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1144
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1147
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1148
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1149
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1150
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1151
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1152
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1156
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1157
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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1168
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1169
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1170
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1171
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1173
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1174
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1175
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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1186
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1188
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1190
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1191
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1192
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1193
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1194
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1195
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1196
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1198
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1199
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1200
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1201
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1202
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1203
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1204
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1205
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1206
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1207
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1208
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1209
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1210
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1211
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1212
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1213
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1214
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1215
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1216
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1218
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1219
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1220
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1221
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1222
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1223
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1224
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1225
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1226
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1227
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1228
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1229
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1230
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1231
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1232
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1233
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1234
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1235
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1236
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1237
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1238
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1239
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1240
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1241
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1242
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1243
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1244
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1245
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1246
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1248
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1249
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1250
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1251
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1252
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1253
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1255
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1256
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1258
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1259
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1260
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1261
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1262
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1263
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1264
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1265
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1266
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1267
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1268
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1269
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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1281
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1282
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1283
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1284
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1285
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1286
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1287
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1288
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1289
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1291
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1292
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1293
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1294
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1295
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1296
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1297
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1298
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1299
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1300
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1301
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1302
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1303
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1304
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1305
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1306
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1307
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<code>BOVIN</code>
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1308
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1309
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1310
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1311
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1312
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1313
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1314
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1315
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1316
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1317
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|
1318
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1319
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1320
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<code>MOUSE</code>
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1321
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1322
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1323
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1324
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1325
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1326
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1327
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<code>HUMAN</code>
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1328
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1329
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1330
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1331
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1332
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+
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1333
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1334
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1335
|
+
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1336
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<speciations>1</speciations>
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1337
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1338
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1339
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<name>171_CHICK</name>
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1340
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1341
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1342
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<code>CHICK</code>
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1343
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1344
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1345
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1346
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1347
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1348
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1349
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<code>XENLA</code>
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1350
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1351
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1352
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1353
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1354
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1355
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1356
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<name>40_CAEEL</name>
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1357
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1358
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<taxonomy>
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|
1359
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<code>CAEEL</code>
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|
1360
|
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1361
|
+
</clade>
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|
1362
|
+
</clade>
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1363
|
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</clade>
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1364
|
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1365
|
+
<clade>
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1366
|
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|
|
1367
|
+
<confidence type="bootstrap">8.0</confidence>
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1368
|
+
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1369
|
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<duplications>1</duplications>
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|
1370
|
+
</events>
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1371
|
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<clade>
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|
1372
|
+
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|
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1373
|
+
<confidence type="bootstrap">6.0</confidence>
|
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1374
|
+
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|
|
1375
|
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<speciations>1</speciations>
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|
1376
|
+
</events>
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1377
|
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<clade>
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1378
|
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|
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1379
|
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<confidence type="bootstrap">15.0</confidence>
|
|
1380
|
+
<events>
|
|
1381
|
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<duplications>1</duplications>
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|
1382
|
+
</events>
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1383
|
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<clade>
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1384
|
+
<branch_length>0.37935</branch_length>
|
|
1385
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1386
|
+
<events>
|
|
1387
|
+
<duplications>1</duplications>
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|
1388
|
+
</events>
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|
1389
|
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<clade>
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|
1390
|
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<branch_length>1.0E-5</branch_length>
|
|
1391
|
+
<confidence type="bootstrap">65.0</confidence>
|
|
1392
|
+
<events>
|
|
1393
|
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<duplications>1</duplications>
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|
1394
|
+
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|
1395
|
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1396
|
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<name>23_BRAFL</name>
|
|
1397
|
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<branch_length>1.0E-5</branch_length>
|
|
1398
|
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<taxonomy>
|
|
1399
|
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<code>BRAFL</code>
|
|
1400
|
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</taxonomy>
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1401
|
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</clade>
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|
1402
|
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<clade>
|
|
1403
|
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<name>24_BRAFL</name>
|
|
1404
|
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<branch_length>0.08958</branch_length>
|
|
1405
|
+
<taxonomy>
|
|
1406
|
+
<code>BRAFL</code>
|
|
1407
|
+
</taxonomy>
|
|
1408
|
+
</clade>
|
|
1409
|
+
</clade>
|
|
1410
|
+
<clade>
|
|
1411
|
+
<name>26_BRAFL</name>
|
|
1412
|
+
<branch_length>1.0E-5</branch_length>
|
|
1413
|
+
<taxonomy>
|
|
1414
|
+
<code>BRAFL</code>
|
|
1415
|
+
</taxonomy>
|
|
1416
|
+
</clade>
|
|
1417
|
+
</clade>
|
|
1418
|
+
<clade>
|
|
1419
|
+
<branch_length>0.07297</branch_length>
|
|
1420
|
+
<confidence type="bootstrap">24.0</confidence>
|
|
1421
|
+
<events>
|
|
1422
|
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<speciations>1</speciations>
|
|
1423
|
+
</events>
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|
1424
|
+
<clade>
|
|
1425
|
+
<branch_length>0.74877</branch_length>
|
|
1426
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1427
|
+
<events>
|
|
1428
|
+
<speciations>1</speciations>
|
|
1429
|
+
</events>
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|
1430
|
+
<clade>
|
|
1431
|
+
<branch_length>0.22523</branch_length>
|
|
1432
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1433
|
+
<events>
|
|
1434
|
+
<speciations>1</speciations>
|
|
1435
|
+
</events>
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|
1436
|
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<clade>
|
|
1437
|
+
<name>168_BRARE</name>
|
|
1438
|
+
<branch_length>0.13915</branch_length>
|
|
1439
|
+
<taxonomy>
|
|
1440
|
+
<code>BRARE</code>
|
|
1441
|
+
</taxonomy>
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|
1442
|
+
</clade>
|
|
1443
|
+
<clade>
|
|
1444
|
+
<name>131_TETNG</name>
|
|
1445
|
+
<branch_length>0.07883</branch_length>
|
|
1446
|
+
<taxonomy>
|
|
1447
|
+
<code>TETNG</code>
|
|
1448
|
+
</taxonomy>
|
|
1449
|
+
</clade>
|
|
1450
|
+
</clade>
|
|
1451
|
+
<clade>
|
|
1452
|
+
<name>146_XENLA</name>
|
|
1453
|
+
<branch_length>0.27947</branch_length>
|
|
1454
|
+
<taxonomy>
|
|
1455
|
+
<code>XENLA</code>
|
|
1456
|
+
</taxonomy>
|
|
1457
|
+
</clade>
|
|
1458
|
+
</clade>
|
|
1459
|
+
<clade>
|
|
1460
|
+
<name>14_SPHGR</name>
|
|
1461
|
+
<branch_length>0.61862</branch_length>
|
|
1462
|
+
<taxonomy>
|
|
1463
|
+
<code>SPHGR</code>
|
|
1464
|
+
</taxonomy>
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|
1465
|
+
</clade>
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|
1466
|
+
</clade>
|
|
1467
|
+
</clade>
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|
1468
|
+
<clade>
|
|
1469
|
+
<branch_length>0.145</branch_length>
|
|
1470
|
+
<confidence type="bootstrap">29.0</confidence>
|
|
1471
|
+
<events>
|
|
1472
|
+
<duplications>1</duplications>
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|
1473
|
+
</events>
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|
1474
|
+
<clade>
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|
1475
|
+
<branch_length>0.14662</branch_length>
|
|
1476
|
+
<confidence type="bootstrap">25.0</confidence>
|
|
1477
|
+
<events>
|
|
1478
|
+
<duplications>1</duplications>
|
|
1479
|
+
</events>
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|
1480
|
+
<clade>
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|
1481
|
+
<name>35_NEMVE</name>
|
|
1482
|
+
<branch_length>0.49481</branch_length>
|
|
1483
|
+
<taxonomy>
|
|
1484
|
+
<code>NEMVE</code>
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|
1485
|
+
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|
1486
|
+
</clade>
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|
1487
|
+
<clade>
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|
1488
|
+
<name>38_NEMVE</name>
|
|
1489
|
+
<branch_length>0.35293</branch_length>
|
|
1490
|
+
<taxonomy>
|
|
1491
|
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<code>NEMVE</code>
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|
1492
|
+
</taxonomy>
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|
1493
|
+
</clade>
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|
1494
|
+
</clade>
|
|
1495
|
+
<clade>
|
|
1496
|
+
<name>34_NEMVE</name>
|
|
1497
|
+
<branch_length>0.32221</branch_length>
|
|
1498
|
+
<taxonomy>
|
|
1499
|
+
<code>NEMVE</code>
|
|
1500
|
+
</taxonomy>
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|
1501
|
+
</clade>
|
|
1502
|
+
</clade>
|
|
1503
|
+
</clade>
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|
1504
|
+
<clade>
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|
1505
|
+
<branch_length>0.40409</branch_length>
|
|
1506
|
+
<confidence type="bootstrap">89.0</confidence>
|
|
1507
|
+
<events>
|
|
1508
|
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<speciations>1</speciations>
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|
1509
|
+
</events>
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|
1510
|
+
<clade>
|
|
1511
|
+
<branch_length>0.10452</branch_length>
|
|
1512
|
+
<confidence type="bootstrap">28.0</confidence>
|
|
1513
|
+
<events>
|
|
1514
|
+
<duplications>1</duplications>
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|
1515
|
+
</events>
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|
1516
|
+
<clade>
|
|
1517
|
+
<branch_length>0.1139</branch_length>
|
|
1518
|
+
<confidence type="bootstrap">41.0</confidence>
|
|
1519
|
+
<events>
|
|
1520
|
+
<duplications>1</duplications>
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|
1521
|
+
</events>
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|
1522
|
+
<clade>
|
|
1523
|
+
<branch_length>0.18551</branch_length>
|
|
1524
|
+
<confidence type="bootstrap">35.0</confidence>
|
|
1525
|
+
<events>
|
|
1526
|
+
<speciations>1</speciations>
|
|
1527
|
+
</events>
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|
1528
|
+
<clade>
|
|
1529
|
+
<branch_length>0.13606</branch_length>
|
|
1530
|
+
<confidence type="bootstrap">92.0</confidence>
|
|
1531
|
+
<events>
|
|
1532
|
+
<duplications>1</duplications>
|
|
1533
|
+
</events>
|
|
1534
|
+
<clade>
|
|
1535
|
+
<branch_length>0.05378</branch_length>
|
|
1536
|
+
<confidence type="bootstrap">57.0</confidence>
|
|
1537
|
+
<events>
|
|
1538
|
+
<speciations>1</speciations>
|
|
1539
|
+
</events>
|
|
1540
|
+
<clade>
|
|
1541
|
+
<branch_length>0.11874</branch_length>
|
|
1542
|
+
<confidence type="bootstrap">90.0</confidence>
|
|
1543
|
+
<events>
|
|
1544
|
+
<speciations>1</speciations>
|
|
1545
|
+
</events>
|
|
1546
|
+
<clade>
|
|
1547
|
+
<name>110_FUGRU</name>
|
|
1548
|
+
<branch_length>0.56162</branch_length>
|
|
1549
|
+
<taxonomy>
|
|
1550
|
+
<code>FUGRU</code>
|
|
1551
|
+
</taxonomy>
|
|
1552
|
+
</clade>
|
|
1553
|
+
<clade>
|
|
1554
|
+
<name>134_TETNG</name>
|
|
1555
|
+
<branch_length>0.03296</branch_length>
|
|
1556
|
+
<taxonomy>
|
|
1557
|
+
<code>TETNG</code>
|
|
1558
|
+
</taxonomy>
|
|
1559
|
+
</clade>
|
|
1560
|
+
</clade>
|
|
1561
|
+
<clade>
|
|
1562
|
+
<branch_length>0.091</branch_length>
|
|
1563
|
+
<confidence type="bootstrap">66.0</confidence>
|
|
1564
|
+
<events>
|
|
1565
|
+
<speciations>1</speciations>
|
|
1566
|
+
</events>
|
|
1567
|
+
<clade>
|
|
1568
|
+
<branch_length>0.04421</branch_length>
|
|
1569
|
+
<confidence type="bootstrap">62.0</confidence>
|
|
1570
|
+
<events>
|
|
1571
|
+
<speciations>1</speciations>
|
|
1572
|
+
</events>
|
|
1573
|
+
<clade>
|
|
1574
|
+
<branch_length>0.13167</branch_length>
|
|
1575
|
+
<confidence type="bootstrap">94.0</confidence>
|
|
1576
|
+
<events>
|
|
1577
|
+
<duplications>1</duplications>
|
|
1578
|
+
</events>
|
|
1579
|
+
<clade>
|
|
1580
|
+
<name>7_HUMAN</name>
|
|
1581
|
+
<branch_length>1.0E-5</branch_length>
|
|
1582
|
+
<taxonomy>
|
|
1583
|
+
<code>HUMAN</code>
|
|
1584
|
+
</taxonomy>
|
|
1585
|
+
</clade>
|
|
1586
|
+
<clade>
|
|
1587
|
+
<branch_length>0.01865</branch_length>
|
|
1588
|
+
<confidence type="bootstrap">61.0</confidence>
|
|
1589
|
+
<events>
|
|
1590
|
+
<speciations>1</speciations>
|
|
1591
|
+
</events>
|
|
1592
|
+
<clade>
|
|
1593
|
+
<branch_length>0.51198</branch_length>
|
|
1594
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1595
|
+
<events>
|
|
1596
|
+
<speciations>1</speciations>
|
|
1597
|
+
</events>
|
|
1598
|
+
<clade>
|
|
1599
|
+
<name>89_CANFA</name>
|
|
1600
|
+
<branch_length>0.01988</branch_length>
|
|
1601
|
+
<taxonomy>
|
|
1602
|
+
<code>CANFA</code>
|
|
1603
|
+
</taxonomy>
|
|
1604
|
+
</clade>
|
|
1605
|
+
<clade>
|
|
1606
|
+
<name>62_BOVIN</name>
|
|
1607
|
+
<branch_length>1.0E-5</branch_length>
|
|
1608
|
+
<taxonomy>
|
|
1609
|
+
<code>BOVIN</code>
|
|
1610
|
+
</taxonomy>
|
|
1611
|
+
</clade>
|
|
1612
|
+
</clade>
|
|
1613
|
+
<clade>
|
|
1614
|
+
<name>114_MOUSE</name>
|
|
1615
|
+
<branch_length>0.01315</branch_length>
|
|
1616
|
+
<taxonomy>
|
|
1617
|
+
<code>MOUSE</code>
|
|
1618
|
+
</taxonomy>
|
|
1619
|
+
</clade>
|
|
1620
|
+
</clade>
|
|
1621
|
+
</clade>
|
|
1622
|
+
<clade>
|
|
1623
|
+
<name>48_CHICK</name>
|
|
1624
|
+
<branch_length>1.0E-5</branch_length>
|
|
1625
|
+
<taxonomy>
|
|
1626
|
+
<code>CHICK</code>
|
|
1627
|
+
</taxonomy>
|
|
1628
|
+
</clade>
|
|
1629
|
+
</clade>
|
|
1630
|
+
<clade>
|
|
1631
|
+
<name>150_XENLA</name>
|
|
1632
|
+
<branch_length>0.0853</branch_length>
|
|
1633
|
+
<taxonomy>
|
|
1634
|
+
<code>XENLA</code>
|
|
1635
|
+
</taxonomy>
|
|
1636
|
+
</clade>
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|
1637
|
+
</clade>
|
|
1638
|
+
</clade>
|
|
1639
|
+
<clade>
|
|
1640
|
+
<branch_length>1.0E-5</branch_length>
|
|
1641
|
+
<confidence type="bootstrap">38.0</confidence>
|
|
1642
|
+
<events>
|
|
1643
|
+
<speciations>1</speciations>
|
|
1644
|
+
</events>
|
|
1645
|
+
<clade>
|
|
1646
|
+
<branch_length>0.19569</branch_length>
|
|
1647
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1648
|
+
<events>
|
|
1649
|
+
<speciations>1</speciations>
|
|
1650
|
+
</events>
|
|
1651
|
+
<clade>
|
|
1652
|
+
<name>101_FUGRU</name>
|
|
1653
|
+
<branch_length>0.02185</branch_length>
|
|
1654
|
+
<taxonomy>
|
|
1655
|
+
<code>FUGRU</code>
|
|
1656
|
+
</taxonomy>
|
|
1657
|
+
</clade>
|
|
1658
|
+
<clade>
|
|
1659
|
+
<name>133_TETNG</name>
|
|
1660
|
+
<branch_length>0.00907</branch_length>
|
|
1661
|
+
<taxonomy>
|
|
1662
|
+
<code>TETNG</code>
|
|
1663
|
+
</taxonomy>
|
|
1664
|
+
</clade>
|
|
1665
|
+
</clade>
|
|
1666
|
+
<clade>
|
|
1667
|
+
<branch_length>0.1765</branch_length>
|
|
1668
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1669
|
+
<events>
|
|
1670
|
+
<duplications>1</duplications>
|
|
1671
|
+
</events>
|
|
1672
|
+
<clade>
|
|
1673
|
+
<name>160_BRARE</name>
|
|
1674
|
+
<branch_length>1.0E-5</branch_length>
|
|
1675
|
+
<taxonomy>
|
|
1676
|
+
<code>BRARE</code>
|
|
1677
|
+
</taxonomy>
|
|
1678
|
+
</clade>
|
|
1679
|
+
<clade>
|
|
1680
|
+
<name>161_BRARE</name>
|
|
1681
|
+
<branch_length>1.0E-5</branch_length>
|
|
1682
|
+
<taxonomy>
|
|
1683
|
+
<code>BRARE</code>
|
|
1684
|
+
</taxonomy>
|
|
1685
|
+
</clade>
|
|
1686
|
+
</clade>
|
|
1687
|
+
</clade>
|
|
1688
|
+
</clade>
|
|
1689
|
+
<clade>
|
|
1690
|
+
<branch_length>0.43964</branch_length>
|
|
1691
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1692
|
+
<events>
|
|
1693
|
+
<duplications>1</duplications>
|
|
1694
|
+
</events>
|
|
1695
|
+
<clade>
|
|
1696
|
+
<name>98_DROME</name>
|
|
1697
|
+
<branch_length>0.38195</branch_length>
|
|
1698
|
+
<taxonomy>
|
|
1699
|
+
<code>DROME</code>
|
|
1700
|
+
</taxonomy>
|
|
1701
|
+
</clade>
|
|
1702
|
+
<clade>
|
|
1703
|
+
<name>99_DROME</name>
|
|
1704
|
+
<branch_length>0.30802</branch_length>
|
|
1705
|
+
<taxonomy>
|
|
1706
|
+
<code>DROME</code>
|
|
1707
|
+
</taxonomy>
|
|
1708
|
+
</clade>
|
|
1709
|
+
</clade>
|
|
1710
|
+
</clade>
|
|
1711
|
+
<clade>
|
|
1712
|
+
<branch_length>0.18404</branch_length>
|
|
1713
|
+
<confidence type="bootstrap">45.0</confidence>
|
|
1714
|
+
<events>
|
|
1715
|
+
<speciations>1</speciations>
|
|
1716
|
+
</events>
|
|
1717
|
+
<clade>
|
|
1718
|
+
<name>22_BRAFL</name>
|
|
1719
|
+
<branch_length>0.39195</branch_length>
|
|
1720
|
+
<taxonomy>
|
|
1721
|
+
<code>BRAFL</code>
|
|
1722
|
+
</taxonomy>
|
|
1723
|
+
</clade>
|
|
1724
|
+
<clade>
|
|
1725
|
+
<name>18_SPHGR</name>
|
|
1726
|
+
<branch_length>0.4734</branch_length>
|
|
1727
|
+
<taxonomy>
|
|
1728
|
+
<code>SPHGR</code>
|
|
1729
|
+
</taxonomy>
|
|
1730
|
+
</clade>
|
|
1731
|
+
</clade>
|
|
1732
|
+
</clade>
|
|
1733
|
+
<clade>
|
|
1734
|
+
<name>20_SPHGR</name>
|
|
1735
|
+
<branch_length>0.64378</branch_length>
|
|
1736
|
+
<taxonomy>
|
|
1737
|
+
<code>SPHGR</code>
|
|
1738
|
+
</taxonomy>
|
|
1739
|
+
</clade>
|
|
1740
|
+
</clade>
|
|
1741
|
+
<clade>
|
|
1742
|
+
<branch_length>0.06108</branch_length>
|
|
1743
|
+
<confidence type="bootstrap">45.0</confidence>
|
|
1744
|
+
<events>
|
|
1745
|
+
<duplications>1</duplications>
|
|
1746
|
+
</events>
|
|
1747
|
+
<clade>
|
|
1748
|
+
<name>39_NEMVE</name>
|
|
1749
|
+
<branch_length>0.56478</branch_length>
|
|
1750
|
+
<taxonomy>
|
|
1751
|
+
<code>NEMVE</code>
|
|
1752
|
+
</taxonomy>
|
|
1753
|
+
</clade>
|
|
1754
|
+
<clade>
|
|
1755
|
+
<branch_length>0.12162</branch_length>
|
|
1756
|
+
<confidence type="bootstrap">57.0</confidence>
|
|
1757
|
+
<events>
|
|
1758
|
+
<duplications>1</duplications>
|
|
1759
|
+
</events>
|
|
1760
|
+
<clade>
|
|
1761
|
+
<branch_length>0.46294</branch_length>
|
|
1762
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1763
|
+
<events>
|
|
1764
|
+
<duplications>1</duplications>
|
|
1765
|
+
</events>
|
|
1766
|
+
<clade>
|
|
1767
|
+
<name>37_NEMVE</name>
|
|
1768
|
+
<branch_length>1.0E-5</branch_length>
|
|
1769
|
+
<taxonomy>
|
|
1770
|
+
<code>NEMVE</code>
|
|
1771
|
+
</taxonomy>
|
|
1772
|
+
</clade>
|
|
1773
|
+
<clade>
|
|
1774
|
+
<name>29_NEMVE</name>
|
|
1775
|
+
<branch_length>1.0E-5</branch_length>
|
|
1776
|
+
<taxonomy>
|
|
1777
|
+
<code>NEMVE</code>
|
|
1778
|
+
</taxonomy>
|
|
1779
|
+
</clade>
|
|
1780
|
+
</clade>
|
|
1781
|
+
<clade>
|
|
1782
|
+
<name>31_NEMVE</name>
|
|
1783
|
+
<branch_length>0.56073</branch_length>
|
|
1784
|
+
<taxonomy>
|
|
1785
|
+
<code>NEMVE</code>
|
|
1786
|
+
</taxonomy>
|
|
1787
|
+
</clade>
|
|
1788
|
+
</clade>
|
|
1789
|
+
</clade>
|
|
1790
|
+
</clade>
|
|
1791
|
+
</clade>
|
|
1792
|
+
</clade>
|
|
1793
|
+
<clade>
|
|
1794
|
+
<branch_length>0.11059</branch_length>
|
|
1795
|
+
<confidence type="bootstrap">29.0</confidence>
|
|
1796
|
+
<events>
|
|
1797
|
+
<duplications>1</duplications>
|
|
1798
|
+
</events>
|
|
1799
|
+
<clade>
|
|
1800
|
+
<branch_length>0.24695</branch_length>
|
|
1801
|
+
<confidence type="bootstrap">52.0</confidence>
|
|
1802
|
+
<events>
|
|
1803
|
+
<duplications>1</duplications>
|
|
1804
|
+
</events>
|
|
1805
|
+
<clade>
|
|
1806
|
+
<name>172_XENLA</name>
|
|
1807
|
+
<branch_length>0.53649</branch_length>
|
|
1808
|
+
<taxonomy>
|
|
1809
|
+
<code>XENLA</code>
|
|
1810
|
+
</taxonomy>
|
|
1811
|
+
</clade>
|
|
1812
|
+
<clade>
|
|
1813
|
+
<branch_length>0.09295</branch_length>
|
|
1814
|
+
<confidence type="bootstrap">50.0</confidence>
|
|
1815
|
+
<events>
|
|
1816
|
+
<duplications>1</duplications>
|
|
1817
|
+
</events>
|
|
1818
|
+
<clade>
|
|
1819
|
+
<branch_length>0.14603</branch_length>
|
|
1820
|
+
<confidence type="bootstrap">87.0</confidence>
|
|
1821
|
+
<events>
|
|
1822
|
+
<speciations>1</speciations>
|
|
1823
|
+
</events>
|
|
1824
|
+
<clade>
|
|
1825
|
+
<branch_length>0.09214</branch_length>
|
|
1826
|
+
<confidence type="bootstrap">65.0</confidence>
|
|
1827
|
+
<events>
|
|
1828
|
+
<speciations>1</speciations>
|
|
1829
|
+
</events>
|
|
1830
|
+
<clade>
|
|
1831
|
+
<name>19_SPHGR</name>
|
|
1832
|
+
<branch_length>0.37571</branch_length>
|
|
1833
|
+
<taxonomy>
|
|
1834
|
+
<code>SPHGR</code>
|
|
1835
|
+
</taxonomy>
|
|
1836
|
+
</clade>
|
|
1837
|
+
<clade>
|
|
1838
|
+
<branch_length>0.09991</branch_length>
|
|
1839
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1840
|
+
<events>
|
|
1841
|
+
<duplications>1</duplications>
|
|
1842
|
+
</events>
|
|
1843
|
+
<clade>
|
|
1844
|
+
<name>28_BRAFL</name>
|
|
1845
|
+
<branch_length>1.0E-5</branch_length>
|
|
1846
|
+
<taxonomy>
|
|
1847
|
+
<code>BRAFL</code>
|
|
1848
|
+
</taxonomy>
|
|
1849
|
+
</clade>
|
|
1850
|
+
<clade>
|
|
1851
|
+
<name>27_BRAFL</name>
|
|
1852
|
+
<branch_length>1.0E-5</branch_length>
|
|
1853
|
+
<taxonomy>
|
|
1854
|
+
<code>BRAFL</code>
|
|
1855
|
+
</taxonomy>
|
|
1856
|
+
</clade>
|
|
1857
|
+
</clade>
|
|
1858
|
+
</clade>
|
|
1859
|
+
<clade>
|
|
1860
|
+
<name>36_NEMVE</name>
|
|
1861
|
+
<branch_length>0.36151</branch_length>
|
|
1862
|
+
<taxonomy>
|
|
1863
|
+
<code>NEMVE</code>
|
|
1864
|
+
</taxonomy>
|
|
1865
|
+
</clade>
|
|
1866
|
+
</clade>
|
|
1867
|
+
<clade>
|
|
1868
|
+
<branch_length>0.34289</branch_length>
|
|
1869
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
1870
|
+
<events>
|
|
1871
|
+
<speciations>1</speciations>
|
|
1872
|
+
</events>
|
|
1873
|
+
<clade>
|
|
1874
|
+
<name>50_CHICK</name>
|
|
1875
|
+
<branch_length>0.05827</branch_length>
|
|
1876
|
+
<taxonomy>
|
|
1877
|
+
<code>CHICK</code>
|
|
1878
|
+
</taxonomy>
|
|
1879
|
+
</clade>
|
|
1880
|
+
<clade>
|
|
1881
|
+
<branch_length>0.22124</branch_length>
|
|
1882
|
+
<confidence type="bootstrap">92.0</confidence>
|
|
1883
|
+
<events>
|
|
1884
|
+
<duplications>1</duplications>
|
|
1885
|
+
</events>
|
|
1886
|
+
<clade>
|
|
1887
|
+
<name>170_MOUSE</name>
|
|
1888
|
+
<branch_length>0.17237</branch_length>
|
|
1889
|
+
<taxonomy>
|
|
1890
|
+
<code>MOUSE</code>
|
|
1891
|
+
</taxonomy>
|
|
1892
|
+
</clade>
|
|
1893
|
+
<clade>
|
|
1894
|
+
<branch_length>1.0E-5</branch_length>
|
|
1895
|
+
<confidence type="bootstrap">59.0</confidence>
|
|
1896
|
+
<events>
|
|
1897
|
+
<duplications>1</duplications>
|
|
1898
|
+
</events>
|
|
1899
|
+
<clade>
|
|
1900
|
+
<name>67_BOVIN</name>
|
|
1901
|
+
<branch_length>0.05006</branch_length>
|
|
1902
|
+
<taxonomy>
|
|
1903
|
+
<code>BOVIN</code>
|
|
1904
|
+
</taxonomy>
|
|
1905
|
+
</clade>
|
|
1906
|
+
<clade>
|
|
1907
|
+
<branch_length>0.00337</branch_length>
|
|
1908
|
+
<confidence type="bootstrap">81.0</confidence>
|
|
1909
|
+
<events>
|
|
1910
|
+
<speciations>1</speciations>
|
|
1911
|
+
</events>
|
|
1912
|
+
<clade>
|
|
1913
|
+
<name>84_CANFA</name>
|
|
1914
|
+
<branch_length>0.01072</branch_length>
|
|
1915
|
+
<taxonomy>
|
|
1916
|
+
<code>CANFA</code>
|
|
1917
|
+
</taxonomy>
|
|
1918
|
+
</clade>
|
|
1919
|
+
<clade>
|
|
1920
|
+
<branch_length>0.02097</branch_length>
|
|
1921
|
+
<confidence type="bootstrap">98.0</confidence>
|
|
1922
|
+
<events>
|
|
1923
|
+
<duplications>1</duplications>
|
|
1924
|
+
</events>
|
|
1925
|
+
<clade>
|
|
1926
|
+
<name>6_HUMAN</name>
|
|
1927
|
+
<branch_length>0.02091</branch_length>
|
|
1928
|
+
<taxonomy>
|
|
1929
|
+
<code>HUMAN</code>
|
|
1930
|
+
</taxonomy>
|
|
1931
|
+
</clade>
|
|
1932
|
+
<clade>
|
|
1933
|
+
<name>5_HUMAN</name>
|
|
1934
|
+
<branch_length>0.01043</branch_length>
|
|
1935
|
+
<taxonomy>
|
|
1936
|
+
<code>HUMAN</code>
|
|
1937
|
+
</taxonomy>
|
|
1938
|
+
</clade>
|
|
1939
|
+
</clade>
|
|
1940
|
+
</clade>
|
|
1941
|
+
</clade>
|
|
1942
|
+
</clade>
|
|
1943
|
+
</clade>
|
|
1944
|
+
</clade>
|
|
1945
|
+
</clade>
|
|
1946
|
+
<clade>
|
|
1947
|
+
<branch_length>0.20775</branch_length>
|
|
1948
|
+
<confidence type="bootstrap">73.0</confidence>
|
|
1949
|
+
<events>
|
|
1950
|
+
<speciations>1</speciations>
|
|
1951
|
+
</events>
|
|
1952
|
+
<clade>
|
|
1953
|
+
<name>32_NEMVE</name>
|
|
1954
|
+
<branch_length>0.30744</branch_length>
|
|
1955
|
+
<taxonomy>
|
|
1956
|
+
<code>NEMVE</code>
|
|
1957
|
+
</taxonomy>
|
|
1958
|
+
</clade>
|
|
1959
|
+
<clade>
|
|
1960
|
+
<branch_length>0.27579</branch_length>
|
|
1961
|
+
<confidence type="bootstrap">64.0</confidence>
|
|
1962
|
+
<events>
|
|
1963
|
+
<speciations>1</speciations>
|
|
1964
|
+
</events>
|
|
1965
|
+
<clade>
|
|
1966
|
+
<name>53_CIOIN</name>
|
|
1967
|
+
<branch_length>0.40206</branch_length>
|
|
1968
|
+
<taxonomy>
|
|
1969
|
+
<code>CIOIN</code>
|
|
1970
|
+
</taxonomy>
|
|
1971
|
+
</clade>
|
|
1972
|
+
<clade>
|
|
1973
|
+
<branch_length>0.28261</branch_length>
|
|
1974
|
+
<confidence type="bootstrap">92.0</confidence>
|
|
1975
|
+
<events>
|
|
1976
|
+
<speciations>1</speciations>
|
|
1977
|
+
</events>
|
|
1978
|
+
<clade>
|
|
1979
|
+
<branch_length>0.05338</branch_length>
|
|
1980
|
+
<confidence type="bootstrap">67.0</confidence>
|
|
1981
|
+
<events>
|
|
1982
|
+
<duplications>1</duplications>
|
|
1983
|
+
</events>
|
|
1984
|
+
<clade>
|
|
1985
|
+
<name>156_BRAREb</name>
|
|
1986
|
+
<branch_length>0.64914</branch_length>
|
|
1987
|
+
<taxonomy>
|
|
1988
|
+
<code>BRARE</code>
|
|
1989
|
+
</taxonomy>
|
|
1990
|
+
</clade>
|
|
1991
|
+
<clade>
|
|
1992
|
+
<branch_length>0.0829</branch_length>
|
|
1993
|
+
<confidence type="bootstrap">70.0</confidence>
|
|
1994
|
+
<events>
|
|
1995
|
+
<speciations>1</speciations>
|
|
1996
|
+
</events>
|
|
1997
|
+
<clade>
|
|
1998
|
+
<name>156_BRAREa</name>
|
|
1999
|
+
<branch_length>0.18704</branch_length>
|
|
2000
|
+
<taxonomy>
|
|
2001
|
+
<code>BRARE</code>
|
|
2002
|
+
</taxonomy>
|
|
2003
|
+
</clade>
|
|
2004
|
+
<clade>
|
|
2005
|
+
<branch_length>0.03919</branch_length>
|
|
2006
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
2007
|
+
<events>
|
|
2008
|
+
<speciations>1</speciations>
|
|
2009
|
+
</events>
|
|
2010
|
+
<clade>
|
|
2011
|
+
<name>138_TETNG</name>
|
|
2012
|
+
<branch_length>0.03397</branch_length>
|
|
2013
|
+
<taxonomy>
|
|
2014
|
+
<code>TETNG</code>
|
|
2015
|
+
</taxonomy>
|
|
2016
|
+
</clade>
|
|
2017
|
+
<clade>
|
|
2018
|
+
<name>173_FUGRU</name>
|
|
2019
|
+
<branch_length>1.0E-5</branch_length>
|
|
2020
|
+
<taxonomy>
|
|
2021
|
+
<code>FUGRU</code>
|
|
2022
|
+
</taxonomy>
|
|
2023
|
+
</clade>
|
|
2024
|
+
</clade>
|
|
2025
|
+
</clade>
|
|
2026
|
+
</clade>
|
|
2027
|
+
<clade>
|
|
2028
|
+
<branch_length>0.15101</branch_length>
|
|
2029
|
+
<confidence type="bootstrap">78.0</confidence>
|
|
2030
|
+
<events>
|
|
2031
|
+
<speciations>1</speciations>
|
|
2032
|
+
</events>
|
|
2033
|
+
<clade>
|
|
2034
|
+
<name>153_XENLA</name>
|
|
2035
|
+
<branch_length>0.15191</branch_length>
|
|
2036
|
+
<taxonomy>
|
|
2037
|
+
<code>XENLA</code>
|
|
2038
|
+
</taxonomy>
|
|
2039
|
+
</clade>
|
|
2040
|
+
<clade>
|
|
2041
|
+
<branch_length>0.24267</branch_length>
|
|
2042
|
+
<confidence type="bootstrap">100.0</confidence>
|
|
2043
|
+
<events>
|
|
2044
|
+
<duplications>1</duplications>
|
|
2045
|
+
</events>
|
|
2046
|
+
<clade>
|
|
2047
|
+
<name>116_MOUSE</name>
|
|
2048
|
+
<branch_length>1.0E-5</branch_length>
|
|
2049
|
+
<taxonomy>
|
|
2050
|
+
<code>MOUSE</code>
|
|
2051
|
+
</taxonomy>
|
|
2052
|
+
</clade>
|
|
2053
|
+
<clade>
|
|
2054
|
+
<branch_length>0.04527</branch_length>
|
|
2055
|
+
<confidence type="bootstrap">49.0</confidence>
|
|
2056
|
+
<events>
|
|
2057
|
+
<speciations>1</speciations>
|
|
2058
|
+
</events>
|
|
2059
|
+
<clade>
|
|
2060
|
+
<name>4_HUMAN</name>
|
|
2061
|
+
<branch_length>1.0E-5</branch_length>
|
|
2062
|
+
<taxonomy>
|
|
2063
|
+
<code>HUMAN</code>
|
|
2064
|
+
</taxonomy>
|
|
2065
|
+
</clade>
|
|
2066
|
+
<clade>
|
|
2067
|
+
<branch_length>0.011</branch_length>
|
|
2068
|
+
<confidence type="bootstrap">37.0</confidence>
|
|
2069
|
+
<events>
|
|
2070
|
+
<speciations>1</speciations>
|
|
2071
|
+
</events>
|
|
2072
|
+
<clade>
|
|
2073
|
+
<name>94_CANFA</name>
|
|
2074
|
+
<branch_length>1.0E-5</branch_length>
|
|
2075
|
+
<taxonomy>
|
|
2076
|
+
<code>CANFA</code>
|
|
2077
|
+
</taxonomy>
|
|
2078
|
+
</clade>
|
|
2079
|
+
<clade>
|
|
2080
|
+
<name>82_BOVIN</name>
|
|
2081
|
+
<branch_length>1.0E-5</branch_length>
|
|
2082
|
+
<taxonomy>
|
|
2083
|
+
<code>BOVIN</code>
|
|
2084
|
+
</taxonomy>
|
|
2085
|
+
</clade>
|
|
2086
|
+
</clade>
|
|
2087
|
+
</clade>
|
|
2088
|
+
</clade>
|
|
2089
|
+
</clade>
|
|
2090
|
+
</clade>
|
|
2091
|
+
</clade>
|
|
2092
|
+
</clade>
|
|
2093
|
+
</clade>
|
|
2094
|
+
</clade>
|
|
2095
|
+
</clade>
|
|
2096
|
+
</phylogeny>
|
|
2097
|
+
</phyloxml>
|