bio 1.5.2 → 1.6.0.pre.20181210
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- checksums.yaml +5 -5
- data/.travis.yml +12 -11
- data/ChangeLog +14 -3106
- data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -1
- data/KNOWN_ISSUES.rdoc +0 -5
- data/README.rdoc +11 -18
- data/RELEASE_NOTES.rdoc +34 -291
- data/Rakefile +13 -9
- data/appveyor.yml +21 -0
- data/bioruby.gemspec +7 -78
- data/bioruby.gemspec.erb +8 -27
- data/doc/ChangeLog-1.5.0 +2919 -0
- data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
- data/doc/Tutorial.rd +6 -108
- data/doc/Tutorial.rd.html +19 -98
- data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
- data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
- data/gemfiles/Gemfile.travis-rbx +0 -1
- data/gemfiles/Gemfile.travis-ruby1.8 +4 -4
- data/gemfiles/Gemfile.travis-ruby1.9 +0 -1
- data/gemfiles/prepare-gemspec.rb +4 -0
- data/lib/bio.rb +0 -10
- data/lib/bio/data/codontable.rb +99 -3
- data/lib/bio/io/togows.rb +5 -5
- data/lib/bio/version.rb +6 -8
- data/sample/test_restriction_enzyme_long.rb +1 -1
- data/test/unit/bio/data/test_codontable.rb +3 -0
- metadata +11 -77
- data/bin/bioruby +0 -47
- data/bin/br_biofetch.rb +0 -71
- data/bin/br_bioflat.rb +0 -293
- data/bin/br_biogetseq.rb +0 -45
- data/bin/br_pmfetch.rb +0 -422
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
- data/lib/bio/db/biosql/sequence.rb +0 -444
- data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
- data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
- data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
- data/lib/bio/io/biosql/ar-biosql.rb +0 -257
- data/lib/bio/io/biosql/biosql.rb +0 -39
- data/lib/bio/io/biosql/config/database.yml +0 -21
- data/lib/bio/io/sql.rb +0 -79
- data/lib/bio/shell.rb +0 -44
- data/lib/bio/shell/core.rb +0 -578
- data/lib/bio/shell/demo.rb +0 -146
- data/lib/bio/shell/interface.rb +0 -217
- data/lib/bio/shell/irb.rb +0 -94
- data/lib/bio/shell/object.rb +0 -71
- data/lib/bio/shell/plugin/blast.rb +0 -42
- data/lib/bio/shell/plugin/codon.rb +0 -218
- data/lib/bio/shell/plugin/das.rb +0 -58
- data/lib/bio/shell/plugin/emboss.rb +0 -23
- data/lib/bio/shell/plugin/entry.rb +0 -137
- data/lib/bio/shell/plugin/flatfile.rb +0 -101
- data/lib/bio/shell/plugin/midi.rb +0 -430
- data/lib/bio/shell/plugin/ncbirest.rb +0 -68
- data/lib/bio/shell/plugin/obda.rb +0 -45
- data/lib/bio/shell/plugin/psort.rb +0 -56
- data/lib/bio/shell/plugin/seq.rb +0 -248
- data/lib/bio/shell/plugin/togows.rb +0 -40
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +0 -25
- data/lib/bio/shell/setup.rb +0 -108
- data/lib/bio/shell/web.rb +0 -102
- data/sample/test_phyloxml_big.rb +0 -205
- data/test/data/phyloxml/apaf.xml +0 -666
- data/test/data/phyloxml/bcl_2.xml +0 -2097
- data/test/data/phyloxml/made_up.xml +0 -144
- data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
- data/test/data/phyloxml/phyloxml_examples.xml +0 -415
- data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
- data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
- data/test/unit/bio/db/test_phyloxml.rb +0 -821
- data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
- data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
- data/test/unit/bio/test_shell.rb +0 -20
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<duplications>1</duplications>
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<clade>
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245
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<name>125_MOUSE</name>
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246
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<branch_length>0.04425</branch_length>
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247
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<taxonomy>
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248
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<code>MOUSE</code>
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249
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</clade>
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251
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<clade>
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<branch_length>0.14928</branch_length>
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253
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<confidence type="bootstrap">40.0</confidence>
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<events>
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<speciations>1</speciations>
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<clade>
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<name>95_CANFA</name>
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<branch_length>0.09977</branch_length>
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<taxonomy>
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261
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<code>CANFA</code>
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<name>13_HUMAN</name>
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266
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<branch_length>0.07433</branch_length>
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<taxonomy>
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<code>HUMAN</code>
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<clade>
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<branch_length>0.57089</branch_length>
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276
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<confidence type="bootstrap">66.0</confidence>
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<events>
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</events>
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<clade>
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281
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<branch_length>0.53798</branch_length>
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282
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<confidence type="bootstrap">100.0</confidence>
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283
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<events>
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284
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<duplications>1</duplications>
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285
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</events>
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<clade>
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<name>16_SPHGR</name>
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<branch_length>1.0E-5</branch_length>
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<taxonomy>
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<code>SPHGR</code>
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<name>17_SPHGR</name>
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<branch_length>1.0E-5</branch_length>
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<taxonomy>
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<code>SPHGR</code>
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</clade>
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<clade>
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302
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<branch_length>0.69471</branch_length>
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303
|
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<confidence type="bootstrap">89.0</confidence>
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304
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<events>
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305
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<speciations>1</speciations>
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306
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</events>
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<clade>
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308
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<branch_length>0.15935</branch_length>
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309
|
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<confidence type="bootstrap">83.0</confidence>
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310
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<events>
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311
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<speciations>1</speciations>
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312
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</events>
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<clade>
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314
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<branch_length>0.24123</branch_length>
|
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315
|
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<confidence type="bootstrap">100.0</confidence>
|
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316
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<events>
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317
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<duplications>1</duplications>
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318
|
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</events>
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<clade>
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<name>158_BRARE</name>
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321
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<branch_length>1.0E-5</branch_length>
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<taxonomy>
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323
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<code>BRARE</code>
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324
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|
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</clade>
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326
|
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<clade>
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327
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<name>169_BRARE</name>
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328
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<branch_length>1.0E-5</branch_length>
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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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</taxonomy>
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332
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</clade>
|
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333
|
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</clade>
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|
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<clade>
|
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335
|
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<name>130_TETNG</name>
|
|
336
|
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<branch_length>0.37777</branch_length>
|
|
337
|
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<taxonomy>
|
|
338
|
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<code>TETNG</code>
|
|
339
|
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</taxonomy>
|
|
340
|
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</clade>
|
|
341
|
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</clade>
|
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342
|
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<clade>
|
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343
|
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<branch_length>0.13835</branch_length>
|
|
344
|
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<confidence type="bootstrap">44.0</confidence>
|
|
345
|
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<events>
|
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346
|
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<speciations>1</speciations>
|
|
347
|
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</events>
|
|
348
|
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<clade>
|
|
349
|
-
<branch_length>0.1765</branch_length>
|
|
350
|
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<confidence type="bootstrap">73.0</confidence>
|
|
351
|
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<events>
|
|
352
|
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<duplications>1</duplications>
|
|
353
|
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</events>
|
|
354
|
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<clade>
|
|
355
|
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<name>122_MOUSE</name>
|
|
356
|
-
<branch_length>0.10759</branch_length>
|
|
357
|
-
<taxonomy>
|
|
358
|
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<code>MOUSE</code>
|
|
359
|
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</taxonomy>
|
|
360
|
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</clade>
|
|
361
|
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<clade>
|
|
362
|
-
<branch_length>0.09256</branch_length>
|
|
363
|
-
<confidence type="bootstrap">44.0</confidence>
|
|
364
|
-
<events>
|
|
365
|
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<speciations>1</speciations>
|
|
366
|
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</events>
|
|
367
|
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<clade>
|
|
368
|
-
<branch_length>0.01016</branch_length>
|
|
369
|
-
<confidence type="bootstrap">40.0</confidence>
|
|
370
|
-
<events>
|
|
371
|
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<duplications>1</duplications>
|
|
372
|
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</events>
|
|
373
|
-
<clade>
|
|
374
|
-
<branch_length>0.0243</branch_length>
|
|
375
|
-
<confidence type="bootstrap">32.0</confidence>
|
|
376
|
-
<events>
|
|
377
|
-
<speciations>1</speciations>
|
|
378
|
-
</events>
|
|
379
|
-
<clade>
|
|
380
|
-
<name>11_HUMAN</name>
|
|
381
|
-
<branch_length>0.02336</branch_length>
|
|
382
|
-
<taxonomy>
|
|
383
|
-
<code>HUMAN</code>
|
|
384
|
-
</taxonomy>
|
|
385
|
-
</clade>
|
|
386
|
-
<clade>
|
|
387
|
-
<name>68_BOVIN</name>
|
|
388
|
-
<branch_length>0.24624</branch_length>
|
|
389
|
-
<taxonomy>
|
|
390
|
-
<code>BOVIN</code>
|
|
391
|
-
</taxonomy>
|
|
392
|
-
</clade>
|
|
393
|
-
</clade>
|
|
394
|
-
<clade>
|
|
395
|
-
<name>92_CANFA</name>
|
|
396
|
-
<branch_length>1.0E-5</branch_length>
|
|
397
|
-
<taxonomy>
|
|
398
|
-
<code>CANFA</code>
|
|
399
|
-
</taxonomy>
|
|
400
|
-
</clade>
|
|
401
|
-
</clade>
|
|
402
|
-
<clade>
|
|
403
|
-
<name>46_CHICK</name>
|
|
404
|
-
<branch_length>1.06707</branch_length>
|
|
405
|
-
<taxonomy>
|
|
406
|
-
<code>CHICK</code>
|
|
407
|
-
</taxonomy>
|
|
408
|
-
</clade>
|
|
409
|
-
</clade>
|
|
410
|
-
</clade>
|
|
411
|
-
<clade>
|
|
412
|
-
<name>147_XENLA</name>
|
|
413
|
-
<branch_length>0.43513</branch_length>
|
|
414
|
-
<taxonomy>
|
|
415
|
-
<code>XENLA</code>
|
|
416
|
-
</taxonomy>
|
|
417
|
-
</clade>
|
|
418
|
-
</clade>
|
|
419
|
-
</clade>
|
|
420
|
-
</clade>
|
|
421
|
-
</clade>
|
|
422
|
-
<clade>
|
|
423
|
-
<branch_length>0.21984499999999996</branch_length>
|
|
424
|
-
<confidence type="bootstrap">33.0</confidence>
|
|
425
|
-
<events>
|
|
426
|
-
<duplications>1</duplications>
|
|
427
|
-
</events>
|
|
428
|
-
<clade>
|
|
429
|
-
<branch_length>0.13885</branch_length>
|
|
430
|
-
<confidence type="bootstrap">14.0</confidence>
|
|
431
|
-
<events>
|
|
432
|
-
<duplications>1</duplications>
|
|
433
|
-
</events>
|
|
434
|
-
<clade>
|
|
435
|
-
<branch_length>0.07066</branch_length>
|
|
436
|
-
<confidence type="bootstrap">2.0</confidence>
|
|
437
|
-
<events>
|
|
438
|
-
<duplications>1</duplications>
|
|
439
|
-
</events>
|
|
440
|
-
<clade>
|
|
441
|
-
<branch_length>0.0137</branch_length>
|
|
442
|
-
<confidence type="bootstrap">3.0</confidence>
|
|
443
|
-
<events>
|
|
444
|
-
<speciations>1</speciations>
|
|
445
|
-
</events>
|
|
446
|
-
<clade>
|
|
447
|
-
<branch_length>0.10632</branch_length>
|
|
448
|
-
<confidence type="bootstrap">4.0</confidence>
|
|
449
|
-
<events>
|
|
450
|
-
<duplications>1</duplications>
|
|
451
|
-
</events>
|
|
452
|
-
<clade>
|
|
453
|
-
<branch_length>0.09782</branch_length>
|
|
454
|
-
<confidence type="bootstrap">15.0</confidence>
|
|
455
|
-
<events>
|
|
456
|
-
<speciations>1</speciations>
|
|
457
|
-
</events>
|
|
458
|
-
<clade>
|
|
459
|
-
<branch_length>0.08093</branch_length>
|
|
460
|
-
<confidence type="bootstrap">32.0</confidence>
|
|
461
|
-
<events>
|
|
462
|
-
<speciations>1</speciations>
|
|
463
|
-
</events>
|
|
464
|
-
<clade>
|
|
465
|
-
<branch_length>0.17228</branch_length>
|
|
466
|
-
<confidence type="bootstrap">52.0</confidence>
|
|
467
|
-
<events>
|
|
468
|
-
<duplications>1</duplications>
|
|
469
|
-
</events>
|
|
470
|
-
<clade>
|
|
471
|
-
<branch_length>0.22305</branch_length>
|
|
472
|
-
<confidence type="bootstrap">76.0</confidence>
|
|
473
|
-
<events>
|
|
474
|
-
<duplications>1</duplications>
|
|
475
|
-
</events>
|
|
476
|
-
<clade>
|
|
477
|
-
<branch_length>0.00625</branch_length>
|
|
478
|
-
<confidence type="bootstrap">55.0</confidence>
|
|
479
|
-
<events>
|
|
480
|
-
<speciations>1</speciations>
|
|
481
|
-
</events>
|
|
482
|
-
<clade>
|
|
483
|
-
<name>140_TETNG</name>
|
|
484
|
-
<branch_length>0.92309</branch_length>
|
|
485
|
-
<taxonomy>
|
|
486
|
-
<code>TETNG</code>
|
|
487
|
-
</taxonomy>
|
|
488
|
-
</clade>
|
|
489
|
-
<clade>
|
|
490
|
-
<branch_length>0.07662</branch_length>
|
|
491
|
-
<confidence type="bootstrap">43.0</confidence>
|
|
492
|
-
<events>
|
|
493
|
-
<speciations>1</speciations>
|
|
494
|
-
</events>
|
|
495
|
-
<clade>
|
|
496
|
-
<name>152_XENLA</name>
|
|
497
|
-
<branch_length>0.19286</branch_length>
|
|
498
|
-
<taxonomy>
|
|
499
|
-
<code>XENLA</code>
|
|
500
|
-
</taxonomy>
|
|
501
|
-
</clade>
|
|
502
|
-
<clade>
|
|
503
|
-
<branch_length>0.0429</branch_length>
|
|
504
|
-
<confidence type="bootstrap">35.0</confidence>
|
|
505
|
-
<events>
|
|
506
|
-
<speciations>1</speciations>
|
|
507
|
-
</events>
|
|
508
|
-
<clade>
|
|
509
|
-
<branch_length>0.06125</branch_length>
|
|
510
|
-
<confidence type="bootstrap">68.0</confidence>
|
|
511
|
-
<events>
|
|
512
|
-
<duplications>1</duplications>
|
|
513
|
-
</events>
|
|
514
|
-
<clade>
|
|
515
|
-
<branch_length>1.0E-5</branch_length>
|
|
516
|
-
<confidence type="bootstrap">93.0</confidence>
|
|
517
|
-
<events>
|
|
518
|
-
<duplications>1</duplications>
|
|
519
|
-
</events>
|
|
520
|
-
<clade>
|
|
521
|
-
<branch_length>1.0E-5</branch_length>
|
|
522
|
-
<confidence type="bootstrap">75.0</confidence>
|
|
523
|
-
<events>
|
|
524
|
-
<speciations>1</speciations>
|
|
525
|
-
</events>
|
|
526
|
-
<clade>
|
|
527
|
-
<name>0_HUMAN</name>
|
|
528
|
-
<branch_length>1.0E-5</branch_length>
|
|
529
|
-
<taxonomy>
|
|
530
|
-
<code>HUMAN</code>
|
|
531
|
-
</taxonomy>
|
|
532
|
-
</clade>
|
|
533
|
-
<clade>
|
|
534
|
-
<name>72_BOVIN</name>
|
|
535
|
-
<branch_length>0.0105</branch_length>
|
|
536
|
-
<taxonomy>
|
|
537
|
-
<code>BOVIN</code>
|
|
538
|
-
</taxonomy>
|
|
539
|
-
</clade>
|
|
540
|
-
</clade>
|
|
541
|
-
<clade>
|
|
542
|
-
<name>123_MOUSE</name>
|
|
543
|
-
<branch_length>0.01053</branch_length>
|
|
544
|
-
<taxonomy>
|
|
545
|
-
<code>MOUSE</code>
|
|
546
|
-
</taxonomy>
|
|
547
|
-
</clade>
|
|
548
|
-
</clade>
|
|
549
|
-
<clade>
|
|
550
|
-
<name>97_CANFA</name>
|
|
551
|
-
<branch_length>1.0E-5</branch_length>
|
|
552
|
-
<taxonomy>
|
|
553
|
-
<code>CANFA</code>
|
|
554
|
-
</taxonomy>
|
|
555
|
-
</clade>
|
|
556
|
-
</clade>
|
|
557
|
-
<clade>
|
|
558
|
-
<name>41_CHICK</name>
|
|
559
|
-
<branch_length>0.03818</branch_length>
|
|
560
|
-
<taxonomy>
|
|
561
|
-
<code>CHICK</code>
|
|
562
|
-
</taxonomy>
|
|
563
|
-
</clade>
|
|
564
|
-
</clade>
|
|
565
|
-
</clade>
|
|
566
|
-
</clade>
|
|
567
|
-
<clade>
|
|
568
|
-
<branch_length>0.07344</branch_length>
|
|
569
|
-
<confidence type="bootstrap">38.0</confidence>
|
|
570
|
-
<events>
|
|
571
|
-
<speciations>1</speciations>
|
|
572
|
-
</events>
|
|
573
|
-
<clade>
|
|
574
|
-
<branch_length>0.18878</branch_length>
|
|
575
|
-
<confidence type="bootstrap">96.0</confidence>
|
|
576
|
-
<events>
|
|
577
|
-
<speciations>1</speciations>
|
|
578
|
-
</events>
|
|
579
|
-
<clade>
|
|
580
|
-
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581
|
-
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582
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-
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583
|
-
<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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-
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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
|
-
<taxonomy>
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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
|
-
<taxonomy>
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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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-
</clade>
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607
|
-
</clade>
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608
|
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<clade>
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609
|
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610
|
-
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611
|
-
<taxonomy>
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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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<duplications>1</duplications>
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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
|
-
<speciations>1</speciations>
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|
628
|
-
</events>
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|
629
|
-
<clade>
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630
|
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631
|
-
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632
|
-
<taxonomy>
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633
|
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<code>XENLA</code>
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634
|
-
</taxonomy>
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635
|
-
</clade>
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636
|
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<clade>
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637
|
-
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|
638
|
-
<confidence type="bootstrap">100.0</confidence>
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|
639
|
-
<events>
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|
640
|
-
<duplications>1</duplications>
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|
641
|
-
</events>
|
|
642
|
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<clade>
|
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643
|
-
<name>126_MOUSE</name>
|
|
644
|
-
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|
645
|
-
<taxonomy>
|
|
646
|
-
<code>MOUSE</code>
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|
647
|
-
</taxonomy>
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|
648
|
-
</clade>
|
|
649
|
-
<clade>
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|
650
|
-
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|
|
651
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
652
|
-
<events>
|
|
653
|
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<duplications>1</duplications>
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|
654
|
-
</events>
|
|
655
|
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<clade>
|
|
656
|
-
<name>96_CANFA</name>
|
|
657
|
-
<branch_length>1.0E-5</branch_length>
|
|
658
|
-
<taxonomy>
|
|
659
|
-
<code>CANFA</code>
|
|
660
|
-
</taxonomy>
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|
661
|
-
</clade>
|
|
662
|
-
<clade>
|
|
663
|
-
<branch_length>1.0E-5</branch_length>
|
|
664
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
665
|
-
<events>
|
|
666
|
-
<speciations>1</speciations>
|
|
667
|
-
</events>
|
|
668
|
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<clade>
|
|
669
|
-
<name>8_HUMAN</name>
|
|
670
|
-
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|
|
671
|
-
<taxonomy>
|
|
672
|
-
<code>HUMAN</code>
|
|
673
|
-
</taxonomy>
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|
674
|
-
</clade>
|
|
675
|
-
<clade>
|
|
676
|
-
<name>79_BOVIN</name>
|
|
677
|
-
<branch_length>1.0E-5</branch_length>
|
|
678
|
-
<taxonomy>
|
|
679
|
-
<code>BOVIN</code>
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|
680
|
-
</taxonomy>
|
|
681
|
-
</clade>
|
|
682
|
-
</clade>
|
|
683
|
-
</clade>
|
|
684
|
-
</clade>
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685
|
-
</clade>
|
|
686
|
-
<clade>
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|
687
|
-
<branch_length>0.04974</branch_length>
|
|
688
|
-
<confidence type="bootstrap">25.0</confidence>
|
|
689
|
-
<events>
|
|
690
|
-
<speciations>1</speciations>
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|
691
|
-
</events>
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|
692
|
-
<clade>
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|
693
|
-
<branch_length>0.20281</branch_length>
|
|
694
|
-
<confidence type="bootstrap">86.0</confidence>
|
|
695
|
-
<events>
|
|
696
|
-
<duplications>1</duplications>
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|
697
|
-
</events>
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|
698
|
-
<clade>
|
|
699
|
-
<branch_length>1.0E-5</branch_length>
|
|
700
|
-
<confidence type="bootstrap">92.0</confidence>
|
|
701
|
-
<events>
|
|
702
|
-
<speciations>1</speciations>
|
|
703
|
-
</events>
|
|
704
|
-
<clade>
|
|
705
|
-
<name>164_BRARE</name>
|
|
706
|
-
<branch_length>0.02901</branch_length>
|
|
707
|
-
<taxonomy>
|
|
708
|
-
<code>BRARE</code>
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|
709
|
-
</taxonomy>
|
|
710
|
-
</clade>
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|
711
|
-
<clade>
|
|
712
|
-
<branch_length>0.06877</branch_length>
|
|
713
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
714
|
-
<events>
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|
715
|
-
<speciations>1</speciations>
|
|
716
|
-
</events>
|
|
717
|
-
<clade>
|
|
718
|
-
<name>136_TETNG</name>
|
|
719
|
-
<branch_length>0.01045</branch_length>
|
|
720
|
-
<taxonomy>
|
|
721
|
-
<code>TETNG</code>
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|
722
|
-
</taxonomy>
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|
723
|
-
</clade>
|
|
724
|
-
<clade>
|
|
725
|
-
<name>100_FUGRU</name>
|
|
726
|
-
<branch_length>1.0E-5</branch_length>
|
|
727
|
-
<taxonomy>
|
|
728
|
-
<code>FUGRU</code>
|
|
729
|
-
</taxonomy>
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|
730
|
-
</clade>
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|
731
|
-
</clade>
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|
732
|
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</clade>
|
|
733
|
-
<clade>
|
|
734
|
-
<branch_length>0.17649</branch_length>
|
|
735
|
-
<confidence type="bootstrap">84.0</confidence>
|
|
736
|
-
<events>
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|
737
|
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<duplications>1</duplications>
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|
738
|
-
</events>
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|
739
|
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<clade>
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|
740
|
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<branch_length>0.05352</branch_length>
|
|
741
|
-
<confidence type="bootstrap">97.0</confidence>
|
|
742
|
-
<events>
|
|
743
|
-
<speciations>1</speciations>
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|
744
|
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</events>
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|
745
|
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<clade>
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|
746
|
-
<name>129_TETNG</name>
|
|
747
|
-
<branch_length>6.9E-4</branch_length>
|
|
748
|
-
<taxonomy>
|
|
749
|
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<code>TETNG</code>
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|
750
|
-
</taxonomy>
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|
751
|
-
</clade>
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|
752
|
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<clade>
|
|
753
|
-
<name>104_FUGRU</name>
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|
754
|
-
<branch_length>0.03078</branch_length>
|
|
755
|
-
<taxonomy>
|
|
756
|
-
<code>FUGRU</code>
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|
757
|
-
</taxonomy>
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|
758
|
-
</clade>
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759
|
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</clade>
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|
760
|
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<clade>
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|
761
|
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<branch_length>0.23291</branch_length>
|
|
762
|
-
<confidence type="bootstrap">95.0</confidence>
|
|
763
|
-
<events>
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|
764
|
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<speciations>1</speciations>
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|
765
|
-
</events>
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|
766
|
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<clade>
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767
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<name>128_TETNG</name>
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|
768
|
-
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|
|
769
|
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<taxonomy>
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|
770
|
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<code>TETNG</code>
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|
771
|
-
</taxonomy>
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|
772
|
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</clade>
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|
773
|
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<clade>
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|
774
|
-
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|
|
775
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
776
|
-
<events>
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|
777
|
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<duplications>1</duplications>
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|
778
|
-
</events>
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|
779
|
-
<clade>
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|
780
|
-
<name>103_FUGRU</name>
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|
781
|
-
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|
|
782
|
-
<taxonomy>
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|
783
|
-
<code>FUGRU</code>
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|
784
|
-
</taxonomy>
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785
|
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</clade>
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|
786
|
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<clade>
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|
787
|
-
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|
|
788
|
-
<confidence type="bootstrap">65.0</confidence>
|
|
789
|
-
<events>
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|
790
|
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<duplications>1</duplications>
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|
791
|
-
</events>
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|
792
|
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<clade>
|
|
793
|
-
<name>106_FUGRU</name>
|
|
794
|
-
<branch_length>0.04182</branch_length>
|
|
795
|
-
<taxonomy>
|
|
796
|
-
<code>FUGRU</code>
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|
797
|
-
</taxonomy>
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|
798
|
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</clade>
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|
799
|
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<clade>
|
|
800
|
-
<branch_length>1.0E-5</branch_length>
|
|
801
|
-
<confidence type="bootstrap">77.0</confidence>
|
|
802
|
-
<events>
|
|
803
|
-
<duplications>1</duplications>
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|
804
|
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</events>
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|
805
|
-
<clade>
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|
806
|
-
<branch_length>0.0141</branch_length>
|
|
807
|
-
<confidence type="bootstrap">71.0</confidence>
|
|
808
|
-
<events>
|
|
809
|
-
<duplications>1</duplications>
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|
810
|
-
</events>
|
|
811
|
-
<clade>
|
|
812
|
-
<name>112_FUGRU</name>
|
|
813
|
-
<branch_length>0.03123</branch_length>
|
|
814
|
-
<taxonomy>
|
|
815
|
-
<code>FUGRU</code>
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|
816
|
-
</taxonomy>
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|
817
|
-
</clade>
|
|
818
|
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<clade>
|
|
819
|
-
<name>113_FUGRU</name>
|
|
820
|
-
<branch_length>0.09693</branch_length>
|
|
821
|
-
<taxonomy>
|
|
822
|
-
<code>FUGRU</code>
|
|
823
|
-
</taxonomy>
|
|
824
|
-
</clade>
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|
825
|
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</clade>
|
|
826
|
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<clade>
|
|
827
|
-
<branch_length>0.195</branch_length>
|
|
828
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
829
|
-
<events>
|
|
830
|
-
<duplications>1</duplications>
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|
831
|
-
</events>
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|
832
|
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<clade>
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|
833
|
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<name>108_FUGRU</name>
|
|
834
|
-
<branch_length>0.01027</branch_length>
|
|
835
|
-
<taxonomy>
|
|
836
|
-
<code>FUGRU</code>
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|
837
|
-
</taxonomy>
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|
838
|
-
</clade>
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|
839
|
-
<clade>
|
|
840
|
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<name>111_FUGRU</name>
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|
841
|
-
<branch_length>0.01081</branch_length>
|
|
842
|
-
<taxonomy>
|
|
843
|
-
<code>FUGRU</code>
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|
844
|
-
</taxonomy>
|
|
845
|
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</clade>
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|
846
|
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</clade>
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|
847
|
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</clade>
|
|
848
|
-
</clade>
|
|
849
|
-
</clade>
|
|
850
|
-
</clade>
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|
851
|
-
</clade>
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|
852
|
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</clade>
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|
853
|
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<clade>
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|
854
|
-
<branch_length>0.03668</branch_length>
|
|
855
|
-
<confidence type="bootstrap">58.0</confidence>
|
|
856
|
-
<events>
|
|
857
|
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<speciations>1</speciations>
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|
858
|
-
</events>
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|
859
|
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<clade>
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|
860
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<name>149_XENLA</name>
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|
861
|
-
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|
|
862
|
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<taxonomy>
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|
863
|
-
<code>XENLA</code>
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|
864
|
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</taxonomy>
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|
865
|
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</clade>
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|
866
|
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<clade>
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|
867
|
-
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|
|
868
|
-
<confidence type="bootstrap">90.0</confidence>
|
|
869
|
-
<events>
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|
870
|
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<speciations>1</speciations>
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|
871
|
-
</events>
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|
872
|
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<clade>
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|
873
|
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|
874
|
-
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|
|
875
|
-
<taxonomy>
|
|
876
|
-
<code>CHICK</code>
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|
877
|
-
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|
878
|
-
</clade>
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|
879
|
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<clade>
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|
880
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-
<branch_length>0.03275</branch_length>
|
|
881
|
-
<confidence type="bootstrap">83.0</confidence>
|
|
882
|
-
<events>
|
|
883
|
-
<duplications>1</duplications>
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|
884
|
-
</events>
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|
885
|
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<clade>
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|
886
|
-
<branch_length>0.192</branch_length>
|
|
887
|
-
<confidence type="bootstrap">99.0</confidence>
|
|
888
|
-
<events>
|
|
889
|
-
<duplications>1</duplications>
|
|
890
|
-
</events>
|
|
891
|
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<clade>
|
|
892
|
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<name>63_BOVIN</name>
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|
893
|
-
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|
|
894
|
-
<taxonomy>
|
|
895
|
-
<code>BOVIN</code>
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|
896
|
-
</taxonomy>
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|
897
|
-
</clade>
|
|
898
|
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<clade>
|
|
899
|
-
<name>80_BOVIN</name>
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|
900
|
-
<branch_length>0.13424</branch_length>
|
|
901
|
-
<taxonomy>
|
|
902
|
-
<code>BOVIN</code>
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|
903
|
-
</taxonomy>
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|
904
|
-
</clade>
|
|
905
|
-
</clade>
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|
906
|
-
<clade>
|
|
907
|
-
<branch_length>1.0E-5</branch_length>
|
|
908
|
-
<confidence type="bootstrap">51.0</confidence>
|
|
909
|
-
<events>
|
|
910
|
-
<duplications>1</duplications>
|
|
911
|
-
</events>
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|
912
|
-
<clade>
|
|
913
|
-
<name>57_BOVIN</name>
|
|
914
|
-
<branch_length>0.01041</branch_length>
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|
915
|
-
<taxonomy>
|
|
916
|
-
<code>BOVIN</code>
|
|
917
|
-
</taxonomy>
|
|
918
|
-
</clade>
|
|
919
|
-
<clade>
|
|
920
|
-
<branch_length>1.0E-5</branch_length>
|
|
921
|
-
<confidence type="bootstrap">20.0</confidence>
|
|
922
|
-
<events>
|
|
923
|
-
<duplications>1</duplications>
|
|
924
|
-
</events>
|
|
925
|
-
<clade>
|
|
926
|
-
<name>117_MOUSE</name>
|
|
927
|
-
<branch_length>1.0E-5</branch_length>
|
|
928
|
-
<taxonomy>
|
|
929
|
-
<code>MOUSE</code>
|
|
930
|
-
</taxonomy>
|
|
931
|
-
</clade>
|
|
932
|
-
<clade>
|
|
933
|
-
<branch_length>0.01043</branch_length>
|
|
934
|
-
<confidence type="bootstrap">66.0</confidence>
|
|
935
|
-
<events>
|
|
936
|
-
<speciations>1</speciations>
|
|
937
|
-
</events>
|
|
938
|
-
<clade>
|
|
939
|
-
<name>87_CANFA</name>
|
|
940
|
-
<branch_length>1.0E-5</branch_length>
|
|
941
|
-
<taxonomy>
|
|
942
|
-
<code>CANFA</code>
|
|
943
|
-
</taxonomy>
|
|
944
|
-
</clade>
|
|
945
|
-
<clade>
|
|
946
|
-
<name>1_HUMAN</name>
|
|
947
|
-
<branch_length>1.0E-5</branch_length>
|
|
948
|
-
<taxonomy>
|
|
949
|
-
<code>HUMAN</code>
|
|
950
|
-
</taxonomy>
|
|
951
|
-
</clade>
|
|
952
|
-
</clade>
|
|
953
|
-
</clade>
|
|
954
|
-
</clade>
|
|
955
|
-
</clade>
|
|
956
|
-
</clade>
|
|
957
|
-
</clade>
|
|
958
|
-
</clade>
|
|
959
|
-
</clade>
|
|
960
|
-
</clade>
|
|
961
|
-
<clade>
|
|
962
|
-
<name>25_BRAFL</name>
|
|
963
|
-
<branch_length>0.4534</branch_length>
|
|
964
|
-
<taxonomy>
|
|
965
|
-
<code>BRAFL</code>
|
|
966
|
-
</taxonomy>
|
|
967
|
-
</clade>
|
|
968
|
-
</clade>
|
|
969
|
-
<clade>
|
|
970
|
-
<name>15_SPHGR</name>
|
|
971
|
-
<branch_length>0.68488</branch_length>
|
|
972
|
-
<taxonomy>
|
|
973
|
-
<code>SPHGR</code>
|
|
974
|
-
</taxonomy>
|
|
975
|
-
</clade>
|
|
976
|
-
</clade>
|
|
977
|
-
<clade>
|
|
978
|
-
<name>21_SPHGR</name>
|
|
979
|
-
<branch_length>1.05022</branch_length>
|
|
980
|
-
<taxonomy>
|
|
981
|
-
<code>SPHGR</code>
|
|
982
|
-
</taxonomy>
|
|
983
|
-
</clade>
|
|
984
|
-
</clade>
|
|
985
|
-
<clade>
|
|
986
|
-
<branch_length>0.08808</branch_length>
|
|
987
|
-
<confidence type="bootstrap">22.0</confidence>
|
|
988
|
-
<events>
|
|
989
|
-
<duplications>1</duplications>
|
|
990
|
-
</events>
|
|
991
|
-
<clade>
|
|
992
|
-
<name>33_NEMVE</name>
|
|
993
|
-
<branch_length>0.482</branch_length>
|
|
994
|
-
<taxonomy>
|
|
995
|
-
<code>NEMVE</code>
|
|
996
|
-
</taxonomy>
|
|
997
|
-
</clade>
|
|
998
|
-
<clade>
|
|
999
|
-
<name>30_NEMVE</name>
|
|
1000
|
-
<branch_length>0.47217</branch_length>
|
|
1001
|
-
<taxonomy>
|
|
1002
|
-
<code>NEMVE</code>
|
|
1003
|
-
</taxonomy>
|
|
1004
|
-
</clade>
|
|
1005
|
-
</clade>
|
|
1006
|
-
</clade>
|
|
1007
|
-
<clade>
|
|
1008
|
-
<branch_length>0.28685</branch_length>
|
|
1009
|
-
<confidence type="bootstrap">9.0</confidence>
|
|
1010
|
-
<events>
|
|
1011
|
-
<duplications>1</duplications>
|
|
1012
|
-
</events>
|
|
1013
|
-
<clade>
|
|
1014
|
-
<branch_length>0.17977</branch_length>
|
|
1015
|
-
<confidence type="bootstrap">14.0</confidence>
|
|
1016
|
-
<events>
|
|
1017
|
-
<duplications>1</duplications>
|
|
1018
|
-
</events>
|
|
1019
|
-
<clade>
|
|
1020
|
-
<branch_length>0.4495</branch_length>
|
|
1021
|
-
<confidence type="bootstrap">92.0</confidence>
|
|
1022
|
-
<events>
|
|
1023
|
-
<speciations>1</speciations>
|
|
1024
|
-
</events>
|
|
1025
|
-
<clade>
|
|
1026
|
-
<branch_length>0.33029</branch_length>
|
|
1027
|
-
<confidence type="bootstrap">89.0</confidence>
|
|
1028
|
-
<events>
|
|
1029
|
-
<speciations>1</speciations>
|
|
1030
|
-
</events>
|
|
1031
|
-
<clade>
|
|
1032
|
-
<branch_length>0.13116</branch_length>
|
|
1033
|
-
<confidence type="bootstrap">61.0</confidence>
|
|
1034
|
-
<events>
|
|
1035
|
-
<duplications>1</duplications>
|
|
1036
|
-
</events>
|
|
1037
|
-
<clade>
|
|
1038
|
-
<name>165_BRARE</name>
|
|
1039
|
-
<branch_length>0.30255</branch_length>
|
|
1040
|
-
<taxonomy>
|
|
1041
|
-
<code>BRARE</code>
|
|
1042
|
-
</taxonomy>
|
|
1043
|
-
</clade>
|
|
1044
|
-
<clade>
|
|
1045
|
-
<name>162_BRARE</name>
|
|
1046
|
-
<branch_length>0.62996</branch_length>
|
|
1047
|
-
<taxonomy>
|
|
1048
|
-
<code>BRARE</code>
|
|
1049
|
-
</taxonomy>
|
|
1050
|
-
</clade>
|
|
1051
|
-
</clade>
|
|
1052
|
-
<clade>
|
|
1053
|
-
<branch_length>0.22822</branch_length>
|
|
1054
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1055
|
-
<events>
|
|
1056
|
-
<speciations>1</speciations>
|
|
1057
|
-
</events>
|
|
1058
|
-
<clade>
|
|
1059
|
-
<name>137_TETNG</name>
|
|
1060
|
-
<branch_length>0.24501</branch_length>
|
|
1061
|
-
<taxonomy>
|
|
1062
|
-
<code>TETNG</code>
|
|
1063
|
-
</taxonomy>
|
|
1064
|
-
</clade>
|
|
1065
|
-
<clade>
|
|
1066
|
-
<name>107_FUGRU</name>
|
|
1067
|
-
<branch_length>0.04204</branch_length>
|
|
1068
|
-
<taxonomy>
|
|
1069
|
-
<code>FUGRU</code>
|
|
1070
|
-
</taxonomy>
|
|
1071
|
-
</clade>
|
|
1072
|
-
</clade>
|
|
1073
|
-
</clade>
|
|
1074
|
-
<clade>
|
|
1075
|
-
<branch_length>0.25726</branch_length>
|
|
1076
|
-
<confidence type="bootstrap">94.0</confidence>
|
|
1077
|
-
<events>
|
|
1078
|
-
<duplications>1</duplications>
|
|
1079
|
-
</events>
|
|
1080
|
-
<clade>
|
|
1081
|
-
<branch_length>0.15529</branch_length>
|
|
1082
|
-
<confidence type="bootstrap">59.0</confidence>
|
|
1083
|
-
<events>
|
|
1084
|
-
<speciations>1</speciations>
|
|
1085
|
-
</events>
|
|
1086
|
-
<clade>
|
|
1087
|
-
<name>42_CHICK</name>
|
|
1088
|
-
<branch_length>0.29479</branch_length>
|
|
1089
|
-
<taxonomy>
|
|
1090
|
-
<code>CHICK</code>
|
|
1091
|
-
</taxonomy>
|
|
1092
|
-
</clade>
|
|
1093
|
-
<clade>
|
|
1094
|
-
<name>143_XENLA</name>
|
|
1095
|
-
<branch_length>0.60398</branch_length>
|
|
1096
|
-
<taxonomy>
|
|
1097
|
-
<code>XENLA</code>
|
|
1098
|
-
</taxonomy>
|
|
1099
|
-
</clade>
|
|
1100
|
-
</clade>
|
|
1101
|
-
<clade>
|
|
1102
|
-
<branch_length>0.13595</branch_length>
|
|
1103
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1104
|
-
<events>
|
|
1105
|
-
<duplications>1</duplications>
|
|
1106
|
-
</events>
|
|
1107
|
-
<clade>
|
|
1108
|
-
<name>58_BOVIN</name>
|
|
1109
|
-
<branch_length>0.05604</branch_length>
|
|
1110
|
-
<taxonomy>
|
|
1111
|
-
<code>BOVIN</code>
|
|
1112
|
-
</taxonomy>
|
|
1113
|
-
</clade>
|
|
1114
|
-
<clade>
|
|
1115
|
-
<branch_length>1.0E-5</branch_length>
|
|
1116
|
-
<confidence type="bootstrap">60.0</confidence>
|
|
1117
|
-
<events>
|
|
1118
|
-
<duplications>1</duplications>
|
|
1119
|
-
</events>
|
|
1120
|
-
<clade>
|
|
1121
|
-
<branch_length>0.02217</branch_length>
|
|
1122
|
-
<confidence type="bootstrap">78.0</confidence>
|
|
1123
|
-
<events>
|
|
1124
|
-
<duplications>1</duplications>
|
|
1125
|
-
</events>
|
|
1126
|
-
<clade>
|
|
1127
|
-
<branch_length>1.0E-5</branch_length>
|
|
1128
|
-
<confidence type="bootstrap">42.0</confidence>
|
|
1129
|
-
<events>
|
|
1130
|
-
<speciations>1</speciations>
|
|
1131
|
-
</events>
|
|
1132
|
-
<clade>
|
|
1133
|
-
<name>85_CANFA</name>
|
|
1134
|
-
<branch_length>0.01109</branch_length>
|
|
1135
|
-
<taxonomy>
|
|
1136
|
-
<code>CANFA</code>
|
|
1137
|
-
</taxonomy>
|
|
1138
|
-
</clade>
|
|
1139
|
-
<clade>
|
|
1140
|
-
<name>2_HUMAN</name>
|
|
1141
|
-
<branch_length>0.01103</branch_length>
|
|
1142
|
-
<taxonomy>
|
|
1143
|
-
<code>HUMAN</code>
|
|
1144
|
-
</taxonomy>
|
|
1145
|
-
</clade>
|
|
1146
|
-
</clade>
|
|
1147
|
-
<clade>
|
|
1148
|
-
<name>124_MOUSE</name>
|
|
1149
|
-
<branch_length>0.04504</branch_length>
|
|
1150
|
-
<taxonomy>
|
|
1151
|
-
<code>MOUSE</code>
|
|
1152
|
-
</taxonomy>
|
|
1153
|
-
</clade>
|
|
1154
|
-
</clade>
|
|
1155
|
-
<clade>
|
|
1156
|
-
<name>73_BOVIN</name>
|
|
1157
|
-
<branch_length>1.0E-5</branch_length>
|
|
1158
|
-
<taxonomy>
|
|
1159
|
-
<code>BOVIN</code>
|
|
1160
|
-
</taxonomy>
|
|
1161
|
-
</clade>
|
|
1162
|
-
</clade>
|
|
1163
|
-
</clade>
|
|
1164
|
-
</clade>
|
|
1165
|
-
</clade>
|
|
1166
|
-
<clade>
|
|
1167
|
-
<branch_length>0.53052</branch_length>
|
|
1168
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1169
|
-
<events>
|
|
1170
|
-
<speciations>1</speciations>
|
|
1171
|
-
</events>
|
|
1172
|
-
<clade>
|
|
1173
|
-
<name>45_CHICK</name>
|
|
1174
|
-
<branch_length>0.17601</branch_length>
|
|
1175
|
-
<taxonomy>
|
|
1176
|
-
<code>CHICK</code>
|
|
1177
|
-
</taxonomy>
|
|
1178
|
-
</clade>
|
|
1179
|
-
<clade>
|
|
1180
|
-
<branch_length>0.40974</branch_length>
|
|
1181
|
-
<confidence type="bootstrap">98.0</confidence>
|
|
1182
|
-
<events>
|
|
1183
|
-
<duplications>1</duplications>
|
|
1184
|
-
</events>
|
|
1185
|
-
<clade>
|
|
1186
|
-
<branch_length>0.05702</branch_length>
|
|
1187
|
-
<confidence type="bootstrap">52.0</confidence>
|
|
1188
|
-
<events>
|
|
1189
|
-
<speciations>1</speciations>
|
|
1190
|
-
</events>
|
|
1191
|
-
<clade>
|
|
1192
|
-
<name>91_CANFA</name>
|
|
1193
|
-
<branch_length>0.10905</branch_length>
|
|
1194
|
-
<taxonomy>
|
|
1195
|
-
<code>CANFA</code>
|
|
1196
|
-
</taxonomy>
|
|
1197
|
-
</clade>
|
|
1198
|
-
<clade>
|
|
1199
|
-
<branch_length>0.06948</branch_length>
|
|
1200
|
-
<confidence type="bootstrap">63.0</confidence>
|
|
1201
|
-
<events>
|
|
1202
|
-
<speciations>1</speciations>
|
|
1203
|
-
</events>
|
|
1204
|
-
<clade>
|
|
1205
|
-
<branch_length>0.18193</branch_length>
|
|
1206
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1207
|
-
<events>
|
|
1208
|
-
<duplications>1</duplications>
|
|
1209
|
-
</events>
|
|
1210
|
-
<clade>
|
|
1211
|
-
<name>118_MOUSE</name>
|
|
1212
|
-
<branch_length>0.18633</branch_length>
|
|
1213
|
-
<taxonomy>
|
|
1214
|
-
<code>MOUSE</code>
|
|
1215
|
-
</taxonomy>
|
|
1216
|
-
</clade>
|
|
1217
|
-
<clade>
|
|
1218
|
-
<name>127_MOUSE</name>
|
|
1219
|
-
<branch_length>1.0E-5</branch_length>
|
|
1220
|
-
<taxonomy>
|
|
1221
|
-
<code>MOUSE</code>
|
|
1222
|
-
</taxonomy>
|
|
1223
|
-
</clade>
|
|
1224
|
-
</clade>
|
|
1225
|
-
<clade>
|
|
1226
|
-
<name>3_HUMAN</name>
|
|
1227
|
-
<branch_length>0.04341</branch_length>
|
|
1228
|
-
<taxonomy>
|
|
1229
|
-
<code>HUMAN</code>
|
|
1230
|
-
</taxonomy>
|
|
1231
|
-
</clade>
|
|
1232
|
-
</clade>
|
|
1233
|
-
</clade>
|
|
1234
|
-
<clade>
|
|
1235
|
-
<branch_length>0.09486</branch_length>
|
|
1236
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1237
|
-
<events>
|
|
1238
|
-
<duplications>1</duplications>
|
|
1239
|
-
</events>
|
|
1240
|
-
<clade>
|
|
1241
|
-
<name>76_BOVIN</name>
|
|
1242
|
-
<branch_length>1.0E-5</branch_length>
|
|
1243
|
-
<taxonomy>
|
|
1244
|
-
<code>BOVIN</code>
|
|
1245
|
-
</taxonomy>
|
|
1246
|
-
</clade>
|
|
1247
|
-
<clade>
|
|
1248
|
-
<name>71_BOVIN</name>
|
|
1249
|
-
<branch_length>1.0E-5</branch_length>
|
|
1250
|
-
<taxonomy>
|
|
1251
|
-
<code>BOVIN</code>
|
|
1252
|
-
</taxonomy>
|
|
1253
|
-
</clade>
|
|
1254
|
-
</clade>
|
|
1255
|
-
</clade>
|
|
1256
|
-
</clade>
|
|
1257
|
-
</clade>
|
|
1258
|
-
<clade>
|
|
1259
|
-
<branch_length>0.13006</branch_length>
|
|
1260
|
-
<confidence type="bootstrap">23.0</confidence>
|
|
1261
|
-
<events>
|
|
1262
|
-
<speciations>1</speciations>
|
|
1263
|
-
</events>
|
|
1264
|
-
<clade>
|
|
1265
|
-
<branch_length>0.40777</branch_length>
|
|
1266
|
-
<confidence type="bootstrap">73.0</confidence>
|
|
1267
|
-
<events>
|
|
1268
|
-
<speciations>1</speciations>
|
|
1269
|
-
</events>
|
|
1270
|
-
<clade>
|
|
1271
|
-
<branch_length>0.33571</branch_length>
|
|
1272
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1273
|
-
<events>
|
|
1274
|
-
<speciations>1</speciations>
|
|
1275
|
-
</events>
|
|
1276
|
-
<clade>
|
|
1277
|
-
<name>157_BRARE</name>
|
|
1278
|
-
<branch_length>0.2958</branch_length>
|
|
1279
|
-
<taxonomy>
|
|
1280
|
-
<code>BRARE</code>
|
|
1281
|
-
</taxonomy>
|
|
1282
|
-
</clade>
|
|
1283
|
-
<clade>
|
|
1284
|
-
<name>109_FUGRU</name>
|
|
1285
|
-
<branch_length>0.19527</branch_length>
|
|
1286
|
-
<taxonomy>
|
|
1287
|
-
<code>FUGRU</code>
|
|
1288
|
-
</taxonomy>
|
|
1289
|
-
</clade>
|
|
1290
|
-
</clade>
|
|
1291
|
-
<clade>
|
|
1292
|
-
<branch_length>0.1832</branch_length>
|
|
1293
|
-
<confidence type="bootstrap">68.0</confidence>
|
|
1294
|
-
<events>
|
|
1295
|
-
<duplications>1</duplications>
|
|
1296
|
-
</events>
|
|
1297
|
-
<clade>
|
|
1298
|
-
<branch_length>0.78705</branch_length>
|
|
1299
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1300
|
-
<events>
|
|
1301
|
-
<speciations>1</speciations>
|
|
1302
|
-
</events>
|
|
1303
|
-
<clade>
|
|
1304
|
-
<name>55_BOVIN</name>
|
|
1305
|
-
<branch_length>0.43001</branch_length>
|
|
1306
|
-
<taxonomy>
|
|
1307
|
-
<code>BOVIN</code>
|
|
1308
|
-
</taxonomy>
|
|
1309
|
-
</clade>
|
|
1310
|
-
<clade>
|
|
1311
|
-
<branch_length>0.08251</branch_length>
|
|
1312
|
-
<confidence type="bootstrap">65.0</confidence>
|
|
1313
|
-
<events>
|
|
1314
|
-
<speciations>1</speciations>
|
|
1315
|
-
</events>
|
|
1316
|
-
<clade>
|
|
1317
|
-
<name>119_MOUSE</name>
|
|
1318
|
-
<branch_length>0.64738</branch_length>
|
|
1319
|
-
<taxonomy>
|
|
1320
|
-
<code>MOUSE</code>
|
|
1321
|
-
</taxonomy>
|
|
1322
|
-
</clade>
|
|
1323
|
-
<clade>
|
|
1324
|
-
<name>10_HUMAN</name>
|
|
1325
|
-
<branch_length>0.18995</branch_length>
|
|
1326
|
-
<taxonomy>
|
|
1327
|
-
<code>HUMAN</code>
|
|
1328
|
-
</taxonomy>
|
|
1329
|
-
</clade>
|
|
1330
|
-
</clade>
|
|
1331
|
-
</clade>
|
|
1332
|
-
<clade>
|
|
1333
|
-
<branch_length>0.09353</branch_length>
|
|
1334
|
-
<confidence type="bootstrap">48.0</confidence>
|
|
1335
|
-
<events>
|
|
1336
|
-
<speciations>1</speciations>
|
|
1337
|
-
</events>
|
|
1338
|
-
<clade>
|
|
1339
|
-
<name>171_CHICK</name>
|
|
1340
|
-
<branch_length>0.56823</branch_length>
|
|
1341
|
-
<taxonomy>
|
|
1342
|
-
<code>CHICK</code>
|
|
1343
|
-
</taxonomy>
|
|
1344
|
-
</clade>
|
|
1345
|
-
<clade>
|
|
1346
|
-
<name>141_XENLA</name>
|
|
1347
|
-
<branch_length>0.57176</branch_length>
|
|
1348
|
-
<taxonomy>
|
|
1349
|
-
<code>XENLA</code>
|
|
1350
|
-
</taxonomy>
|
|
1351
|
-
</clade>
|
|
1352
|
-
</clade>
|
|
1353
|
-
</clade>
|
|
1354
|
-
</clade>
|
|
1355
|
-
<clade>
|
|
1356
|
-
<name>40_CAEEL</name>
|
|
1357
|
-
<branch_length>1.20795</branch_length>
|
|
1358
|
-
<taxonomy>
|
|
1359
|
-
<code>CAEEL</code>
|
|
1360
|
-
</taxonomy>
|
|
1361
|
-
</clade>
|
|
1362
|
-
</clade>
|
|
1363
|
-
</clade>
|
|
1364
|
-
</clade>
|
|
1365
|
-
<clade>
|
|
1366
|
-
<branch_length>0.09583</branch_length>
|
|
1367
|
-
<confidence type="bootstrap">8.0</confidence>
|
|
1368
|
-
<events>
|
|
1369
|
-
<duplications>1</duplications>
|
|
1370
|
-
</events>
|
|
1371
|
-
<clade>
|
|
1372
|
-
<branch_length>0.03647</branch_length>
|
|
1373
|
-
<confidence type="bootstrap">6.0</confidence>
|
|
1374
|
-
<events>
|
|
1375
|
-
<speciations>1</speciations>
|
|
1376
|
-
</events>
|
|
1377
|
-
<clade>
|
|
1378
|
-
<branch_length>0.15942</branch_length>
|
|
1379
|
-
<confidence type="bootstrap">15.0</confidence>
|
|
1380
|
-
<events>
|
|
1381
|
-
<duplications>1</duplications>
|
|
1382
|
-
</events>
|
|
1383
|
-
<clade>
|
|
1384
|
-
<branch_length>0.37935</branch_length>
|
|
1385
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1386
|
-
<events>
|
|
1387
|
-
<duplications>1</duplications>
|
|
1388
|
-
</events>
|
|
1389
|
-
<clade>
|
|
1390
|
-
<branch_length>1.0E-5</branch_length>
|
|
1391
|
-
<confidence type="bootstrap">65.0</confidence>
|
|
1392
|
-
<events>
|
|
1393
|
-
<duplications>1</duplications>
|
|
1394
|
-
</events>
|
|
1395
|
-
<clade>
|
|
1396
|
-
<name>23_BRAFL</name>
|
|
1397
|
-
<branch_length>1.0E-5</branch_length>
|
|
1398
|
-
<taxonomy>
|
|
1399
|
-
<code>BRAFL</code>
|
|
1400
|
-
</taxonomy>
|
|
1401
|
-
</clade>
|
|
1402
|
-
<clade>
|
|
1403
|
-
<name>24_BRAFL</name>
|
|
1404
|
-
<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
|
-
<speciations>1</speciations>
|
|
1423
|
-
</events>
|
|
1424
|
-
<clade>
|
|
1425
|
-
<branch_length>0.74877</branch_length>
|
|
1426
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1427
|
-
<events>
|
|
1428
|
-
<speciations>1</speciations>
|
|
1429
|
-
</events>
|
|
1430
|
-
<clade>
|
|
1431
|
-
<branch_length>0.22523</branch_length>
|
|
1432
|
-
<confidence type="bootstrap">100.0</confidence>
|
|
1433
|
-
<events>
|
|
1434
|
-
<speciations>1</speciations>
|
|
1435
|
-
</events>
|
|
1436
|
-
<clade>
|
|
1437
|
-
<name>168_BRARE</name>
|
|
1438
|
-
<branch_length>0.13915</branch_length>
|
|
1439
|
-
<taxonomy>
|
|
1440
|
-
<code>BRARE</code>
|
|
1441
|
-
</taxonomy>
|
|
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>
|
|
1465
|
-
</clade>
|
|
1466
|
-
</clade>
|
|
1467
|
-
</clade>
|
|
1468
|
-
<clade>
|
|
1469
|
-
<branch_length>0.145</branch_length>
|
|
1470
|
-
<confidence type="bootstrap">29.0</confidence>
|
|
1471
|
-
<events>
|
|
1472
|
-
<duplications>1</duplications>
|
|
1473
|
-
</events>
|
|
1474
|
-
<clade>
|
|
1475
|
-
<branch_length>0.14662</branch_length>
|
|
1476
|
-
<confidence type="bootstrap">25.0</confidence>
|
|
1477
|
-
<events>
|
|
1478
|
-
<duplications>1</duplications>
|
|
1479
|
-
</events>
|
|
1480
|
-
<clade>
|
|
1481
|
-
<name>35_NEMVE</name>
|
|
1482
|
-
<branch_length>0.49481</branch_length>
|
|
1483
|
-
<taxonomy>
|
|
1484
|
-
<code>NEMVE</code>
|
|
1485
|
-
</taxonomy>
|
|
1486
|
-
</clade>
|
|
1487
|
-
<clade>
|
|
1488
|
-
<name>38_NEMVE</name>
|
|
1489
|
-
<branch_length>0.35293</branch_length>
|
|
1490
|
-
<taxonomy>
|
|
1491
|
-
<code>NEMVE</code>
|
|
1492
|
-
</taxonomy>
|
|
1493
|
-
</clade>
|
|
1494
|
-
</clade>
|
|
1495
|
-
<clade>
|
|
1496
|
-
<name>34_NEMVE</name>
|
|
1497
|
-
<branch_length>0.32221</branch_length>
|
|
1498
|
-
<taxonomy>
|
|
1499
|
-
<code>NEMVE</code>
|
|
1500
|
-
</taxonomy>
|
|
1501
|
-
</clade>
|
|
1502
|
-
</clade>
|
|
1503
|
-
</clade>
|
|
1504
|
-
<clade>
|
|
1505
|
-
<branch_length>0.40409</branch_length>
|
|
1506
|
-
<confidence type="bootstrap">89.0</confidence>
|
|
1507
|
-
<events>
|
|
1508
|
-
<speciations>1</speciations>
|
|
1509
|
-
</events>
|
|
1510
|
-
<clade>
|
|
1511
|
-
<branch_length>0.10452</branch_length>
|
|
1512
|
-
<confidence type="bootstrap">28.0</confidence>
|
|
1513
|
-
<events>
|
|
1514
|
-
<duplications>1</duplications>
|
|
1515
|
-
</events>
|
|
1516
|
-
<clade>
|
|
1517
|
-
<branch_length>0.1139</branch_length>
|
|
1518
|
-
<confidence type="bootstrap">41.0</confidence>
|
|
1519
|
-
<events>
|
|
1520
|
-
<duplications>1</duplications>
|
|
1521
|
-
</events>
|
|
1522
|
-
<clade>
|
|
1523
|
-
<branch_length>0.18551</branch_length>
|
|
1524
|
-
<confidence type="bootstrap">35.0</confidence>
|
|
1525
|
-
<events>
|
|
1526
|
-
<speciations>1</speciations>
|
|
1527
|
-
</events>
|
|
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>
|
|
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>
|