bio 1.5.1 → 2.0.2

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Files changed (128) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +35 -36
  3. data/ChangeLog +911 -2554
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
  5. data/KNOWN_ISSUES.rdoc +10 -13
  6. data/LEGAL +0 -10
  7. data/README.rdoc +40 -96
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +118 -234
  10. data/Rakefile +13 -43
  11. data/appveyor.yml +29 -0
  12. data/bioruby.gemspec +18 -81
  13. data/bioruby.gemspec.erb +8 -28
  14. data/doc/ChangeLog-1.5.0 +2919 -0
  15. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  16. data/doc/Tutorial.rd +6 -108
  17. data/doc/Tutorial.rd.html +19 -98
  18. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  19. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  20. data/gemfiles/Gemfile.travis-rbx +0 -3
  21. data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
  22. data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
  23. data/gemfiles/Gemfile.windows +6 -0
  24. data/gemfiles/prepare-gemspec.rb +4 -0
  25. data/lib/bio.rb +0 -10
  26. data/lib/bio/appl/blast/genomenet.rb +4 -4
  27. data/lib/bio/appl/blast/report.rb +40 -8
  28. data/lib/bio/appl/fasta/format10.rb +2 -1
  29. data/lib/bio/command.rb +10 -0
  30. data/lib/bio/data/codontable.rb +99 -3
  31. data/lib/bio/db/aaindex.rb +74 -5
  32. data/lib/bio/db/gff.rb +3 -1
  33. data/lib/bio/db/kegg/common.rb +14 -0
  34. data/lib/bio/db/kegg/genes.rb +26 -0
  35. data/lib/bio/db/kegg/pathway.rb +5 -11
  36. data/lib/bio/db/soft.rb +2 -2
  37. data/lib/bio/io/flatfile/autodetection.rb +5 -0
  38. data/lib/bio/io/togows.rb +5 -5
  39. data/lib/bio/map.rb +4 -4
  40. data/lib/bio/sequence/format.rb +1 -0
  41. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
  42. data/lib/bio/util/sirna.rb +2 -0
  43. data/lib/bio/version.rb +6 -8
  44. data/sample/color_scheme_aa.rb +82 -0
  45. data/sample/color_scheme_na.rb +5 -6
  46. data/sample/fastq2html.cwl +23 -0
  47. data/sample/fastq2html.rb +94 -0
  48. data/sample/fastq2html.testdata.yaml +5 -0
  49. data/sample/na2aa.cwl +23 -0
  50. data/sample/na2aa.rb +11 -25
  51. data/sample/na2aa.testdata.yaml +7 -0
  52. data/sample/rev_comp.cwl +23 -0
  53. data/sample/rev_comp.rb +20 -0
  54. data/sample/rev_comp.testdata.yaml +7 -0
  55. data/sample/test_restriction_enzyme_long.rb +1 -1
  56. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  57. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  58. data/test/unit/bio/data/test_codontable.rb +3 -0
  59. data/test/unit/bio/db/test_gff.rb +5 -0
  60. data/test/unit/bio/test_alignment.rb +2 -2
  61. metadata +20 -77
  62. data/bin/bioruby +0 -47
  63. data/bin/br_biofetch.rb +0 -71
  64. data/bin/br_bioflat.rb +0 -293
  65. data/bin/br_biogetseq.rb +0 -45
  66. data/bin/br_pmfetch.rb +0 -422
  67. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  68. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  69. data/lib/bio/db/biosql/sequence.rb +0 -444
  70. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  71. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  72. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  73. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  74. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  75. data/lib/bio/io/biosql/biosql.rb +0 -39
  76. data/lib/bio/io/biosql/config/database.yml +0 -21
  77. data/lib/bio/io/sql.rb +0 -79
  78. data/lib/bio/shell.rb +0 -44
  79. data/lib/bio/shell/core.rb +0 -578
  80. data/lib/bio/shell/demo.rb +0 -146
  81. data/lib/bio/shell/interface.rb +0 -217
  82. data/lib/bio/shell/irb.rb +0 -94
  83. data/lib/bio/shell/object.rb +0 -71
  84. data/lib/bio/shell/plugin/blast.rb +0 -42
  85. data/lib/bio/shell/plugin/codon.rb +0 -218
  86. data/lib/bio/shell/plugin/das.rb +0 -58
  87. data/lib/bio/shell/plugin/emboss.rb +0 -23
  88. data/lib/bio/shell/plugin/entry.rb +0 -137
  89. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  90. data/lib/bio/shell/plugin/midi.rb +0 -430
  91. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  92. data/lib/bio/shell/plugin/obda.rb +0 -45
  93. data/lib/bio/shell/plugin/psort.rb +0 -56
  94. data/lib/bio/shell/plugin/seq.rb +0 -248
  95. data/lib/bio/shell/plugin/togows.rb +0 -40
  96. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  97. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  98. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  99. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  100. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  101. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  102. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  103. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  104. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  105. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  106. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  107. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  108. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  109. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  110. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  111. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  112. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  113. data/lib/bio/shell/script.rb +0 -25
  114. data/lib/bio/shell/setup.rb +0 -108
  115. data/lib/bio/shell/web.rb +0 -102
  116. data/sample/test_phyloxml_big.rb +0 -205
  117. data/setup.rb +0 -1600
  118. data/test/data/phyloxml/apaf.xml +0 -666
  119. data/test/data/phyloxml/bcl_2.xml +0 -2097
  120. data/test/data/phyloxml/made_up.xml +0 -144
  121. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  122. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  123. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  124. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  125. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  126. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  127. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  128. data/test/unit/bio/test_shell.rb +0 -20
data/test/data/phyloxml/apaf.xml DELETED
@@ -1,666 +0,0 @@
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- <?xml version="1.0" encoding="UTF-8"?>
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- <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.00/phyloxml.xsd" xmlns="http://www.phyloxml.org">
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- <phylogeny rooted="true">
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- <clade>
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- <confidence type="unknown">32.0</confidence>
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- <confidence type="unknown">100.0</confidence>
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- <clade>
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- <branch_length>0.22058</branch_length>
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- <confidence type="unknown">89.0</confidence>
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- <clade>
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- <confidence type="unknown">100.0</confidence>
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- <clade>
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- <branch_length>0.06584</branch_length>
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- <confidence type="unknown">100.0</confidence>
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- <clade>
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- <branch_length>0.02309</branch_length>
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- <confidence type="unknown">43.0</confidence>
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- <clade>
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- <branch_length>0.0746</branch_length>
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- <confidence type="unknown">100.0</confidence>
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- <clade>
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- <branch_length>0.02365</branch_length>
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- <confidence type="unknown">88.0</confidence>
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- <clade>
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- <name>22_MOUSE</name>
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- <branch_length>0.05998</branch_length>
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- <taxonomy>
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- <code>MOUSE</code>
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- </taxonomy>
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- <sequence>
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- <domain_architecture length="1249">
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- <domain from="6" to="90" confidence="7.0E-26">CARD</domain>
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- <domain from="109" to="414" confidence="7.2E-117">NB-ARC</domain>
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- <domain from="605" to="643" confidence="2.4E-6">WD40</domain>
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- <domain from="647" to="685" confidence="1.1E-12">WD40</domain>
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- <domain from="689" to="729" confidence="2.4E-7">WD40</domain>
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- <domain from="733" to="771" confidence="4.7E-14">WD40</domain>
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- <domain from="872" to="910" confidence="2.5E-8">WD40</domain>
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- <domain from="993" to="1031" confidence="4.6E-6">WD40</domain>
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- <domain from="1075" to="1113" confidence="6.3E-7">WD40</domain>
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- <domain from="1117" to="1155" confidence="1.4E-7">WD40</domain>
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- <domain from="1168" to="1204" confidence="0.3">WD40</domain>
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- </domain_architecture>
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- </sequence>
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- </clade>
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- <clade>
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- <name>Apaf-1_HUMAN</name>
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- <branch_length>0.01825</branch_length>
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- <taxonomy>
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- <code>HUMAN</code>
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- </taxonomy>
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- <sequence>
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- <domain_architecture length="1248">
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- <domain from="6" to="90" confidence="1.1E-25">CARD</domain>
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- <domain from="109" to="414" confidence="3.0E-134">NB-ARC</domain>
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- <domain from="605" to="643" confidence="8.5E-6">WD40</domain>
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- <domain from="647" to="685" confidence="2.5E-11">WD40</domain>
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- <domain from="689" to="729" confidence="2.4E-8">WD40</domain>
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- <domain from="733" to="771" confidence="3.6E-14">WD40</domain>
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- <domain from="872" to="910" confidence="3.8E-8">WD40</domain>
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- <domain from="1075" to="1113" confidence="4.0E-7">WD40</domain>
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- <domain from="1117" to="1155" confidence="5.9E-8">WD40</domain>
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- </domain_architecture>
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- </sequence>
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- </clade>
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- </clade>
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- <clade>
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- <name>12_CANFA</name>
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- <branch_length>0.04683</branch_length>
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- <taxonomy>
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- <code>CANFA</code>
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- </taxonomy>
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- <sequence>
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- <domain_architecture length="1153">
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- <domain from="6" to="90" confidence="4.5E-22">CARD</domain>
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- <domain from="110" to="415" confidence="4.0E-119">NB-ARC</domain>
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- <domain from="597" to="635" confidence="3.9E-5">WD40</domain>
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- <taxonomy>
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- <code>CHICK</code>
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- <sequence>
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- <domain_architecture length="1207">
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- <domain from="6" to="90" confidence="3.6E-21">CARD</domain>
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- <domain from="109" to="414" confidence="3.6E-109">NB-ARC</domain>
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- <domain from="6" to="90" confidence="4.0E-20">CARD</domain>
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- <domain from="109" to="410" confidence="3.1E-56">NB-ARC</domain>
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- <domain from="148" to="298" confidence="0.8">NACHT</domain>
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- <domain from="771" to="809" confidence="2.3E-11">WD40</domain>
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- <domain from="813" to="853" confidence="1.1E-8">WD40</domain>
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248
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249
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250
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251
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252
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253
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254
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255
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256
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258
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259
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260
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261
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262
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263
- <code>STRPU</code>
264
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265
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266
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267
- <domain from="110" to="402" confidence="1.0E-40">NB-ARC</domain>
268
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269
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270
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271
- <domain from="765" to="802" confidence="0.0036">WD40</domain>
272
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273
- <domain from="975" to="1013" confidence="1.9E-5">WD40</domain>
274
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275
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276
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277
- <domain from="1141" to="1177" confidence="0.011">WD40</domain>
278
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279
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280
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281
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282
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283
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284
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285
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286
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287
- <name>26_STRPU</name>
288
- <branch_length>0.36374</branch_length>
289
- <taxonomy>
290
- <code>STRPU</code>
291
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292
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293
- <domain_architecture length="1319">
294
- <domain from="18" to="98" confidence="3.4E-5">Death</domain>
295
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296
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297
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298
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300
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301
- <name>25_STRPU</name>
302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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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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324
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325
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326
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327
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328
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329
- <domain from="7" to="90" confidence="9.2E-14">CARD</domain>
330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
- <domain from="1" to="75" confidence="0.0046">CARD</domain>
343
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344
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
- <name>28_DROPS</name>
360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
- <name>Dark_DROME</name>
372
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373
- <taxonomy>
374
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375
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376
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377
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378
- <domain from="108" to="397" confidence="2.1E-5">NB-ARC</domain>
379
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380
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381
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382
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383
- <clade>
384
- <name>29_AEDAE</name>
385
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386
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387
- <code>AEDAE</code>
388
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389
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390
- <domain_architecture length="423">
391
- <domain from="109" to="421" confidence="9.3E-6">NB-ARC</domain>
392
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393
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394
- </clade>
395
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396
- <clade>
397
- <name>30_TRICA</name>
398
- <branch_length>0.97698</branch_length>
399
- <taxonomy>
400
- <code>TRICA</code>
401
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402
- <sequence>
403
- <domain_architecture length="1279">
404
- <domain from="5" to="81" confidence="0.59">CARD</domain>
405
- <domain from="92" to="400" confidence="9.0E-11">NB-ARC</domain>
406
- <domain from="630" to="668" confidence="1.1E-5">WD40</domain>
407
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408
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409
- </clade>
410
- </clade>
411
- </clade>
412
- <clade>
413
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414
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415
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416
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417
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418
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419
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420
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421
- <clade>
422
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423
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424
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425
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426
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427
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428
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429
- <confidence type="unknown">100.0</confidence>
430
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431
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432
- <branch_length>0.093</branch_length>
433
- <taxonomy>
434
- <code>BRAFL</code>
435
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436
- <sequence>
437
- <domain_architecture length="752">
438
- <domain from="49" to="356" confidence="9.0E-6">NB-ARC</domain>
439
- </domain_architecture>
440
- </sequence>
441
- </clade>
442
- <clade>
443
- <name>35_BRAFL</name>
444
- <branch_length>0.08226</branch_length>
445
- <taxonomy>
446
- <code>BRAFL</code>
447
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448
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449
- <domain_architecture length="753">
450
- <domain from="25" to="105" confidence="0.16">DED</domain>
451
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452
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453
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454
- </clade>
455
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456
- <clade>
457
- <name>8_BRAFL</name>
458
- <branch_length>0.58563</branch_length>
459
- <taxonomy>
460
- <code>BRAFL</code>
461
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462
- <sequence>
463
- <domain_architecture length="916">
464
- <domain from="58" to="369" confidence="8.4E-7">NB-ARC</domain>
465
- </domain_architecture>
466
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467
- </clade>
468
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469
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470
- <branch_length>0.28437</branch_length>
471
- <confidence type="unknown">84.0</confidence>
472
- <clade>
473
- <name>20_NEMVE</name>
474
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475
- <taxonomy>
476
- <code>NEMVE</code>
477
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478
- <sequence>
479
- <domain_architecture length="786">
480
- <domain from="8" to="91" confidence="1.7E-17">DED</domain>
481
- <domain from="8" to="85" confidence="0.37">PAAD_DAPIN</domain>
482
- <domain from="90" to="388" confidence="6.8E-5">NB-ARC</domain>
483
- <domain from="575" to="608" confidence="0.27">TPR_1</domain>
484
- <domain from="657" to="690" confidence="0.22">TPR_2</domain>
485
- <domain from="698" to="731" confidence="4.2E-5">TPR_2</domain>
486
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487
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488
- </clade>
489
- <clade>
490
- <name>21_NEMVE</name>
491
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492
- <taxonomy>
493
- <code>NEMVE</code>
494
- </taxonomy>
495
- <sequence>
496
- <domain_architecture length="1563">
497
- <domain from="234" to="317" confidence="2.3E-14">CARD</domain>
498
- <domain from="238" to="318" confidence="0.5">Death</domain>
499
- <domain from="329" to="619" confidence="0.022">NB-ARC</domain>
500
- <domain from="906" to="939" confidence="0.17">TPR_1</domain>
501
- <domain from="1326" to="1555" confidence="3.2E-26">RVT_1</domain>
502
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503
- </sequence>
504
- </clade>
505
- </clade>
506
- </clade>
507
- <clade>
508
- <name>9_BRAFL</name>
509
- <branch_length>1.09612</branch_length>
510
- <taxonomy>
511
- <code>BRAFL</code>
512
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513
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514
- <domain_architecture length="1011">
515
- <domain from="5" to="321" confidence="5.0E-5">NB-ARC</domain>
516
- <domain from="497" to="616" confidence="1.6">BTAD</domain>
517
- <domain from="500" to="533" confidence="5.6E-4">TPR_1</domain>
518
- <domain from="542" to="575" confidence="0.43">TPR_1</domain>
519
- <domain from="626" to="659" confidence="0.0084">TPR_2</domain>
520
- <domain from="708" to="741" confidence="1.9E-4">TPR_2</domain>
521
- <domain from="708" to="739" confidence="1.3">TPR_3</domain>
522
- <domain from="708" to="733" confidence="0.16">TPR_4</domain>
523
- <domain from="833" to="916" confidence="5.6E-14">Death</domain>
524
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525
- <domain from="930" to="1011" confidence="8.3E-17">Death</domain>
526
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527
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528
- </clade>
529
- </clade>
530
- <clade>
531
- <branch_length>0.34914</branch_length>
532
- <confidence type="unknown">98.0</confidence>
533
- <clade>
534
- <branch_length>0.22189</branch_length>
535
- <confidence type="unknown">95.0</confidence>
536
- <clade>
537
- <name>3_BRAFL</name>
538
- <branch_length>0.48766</branch_length>
539
- <taxonomy>
540
- <code>BRAFL</code>
541
- </taxonomy>
542
- <sequence>
543
- <domain_architecture length="2080">
544
- <domain from="116" to="423" confidence="1.4E-12">NB-ARC</domain>
545
- <domain from="620" to="659" confidence="1.4E-6">WD40</domain>
546
- <domain from="663" to="701" confidence="1.4E-8">WD40</domain>
547
- <domain from="705" to="743" confidence="3.0E-11">WD40</domain>
548
- <domain from="747" to="785" confidence="1.1E-8">WD40</domain>
549
- <domain from="788" to="826" confidence="1.6E-5">WD40</domain>
550
- <domain from="830" to="870" confidence="1.3E-4">WD40</domain>
551
- <domain from="874" to="914" confidence="6.2E-9">WD40</domain>
552
- <domain from="919" to="957" confidence="0.0011">WD40</domain>
553
- <domain from="961" to="1000" confidence="1.8E-8">WD40</domain>
554
- <domain from="1013" to="1051" confidence="1.3E-6">WD40</domain>
555
- <domain from="1055" to="1092" confidence="0.096">WD40</domain>
556
- <domain from="1794" to="1853" confidence="3.6E-4">Collagen</domain>
557
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558
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559
- </clade>
560
- <clade>
561
- <name>2_BRAFL</name>
562
- <branch_length>0.65293</branch_length>
563
- <taxonomy>
564
- <code>BRAFL</code>
565
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566
- <sequence>
567
- <domain_architecture length="1691">
568
- <domain from="162" to="457" confidence="4.4E-10">NB-ARC</domain>
569
- <domain from="640" to="680" confidence="0.0068">WD40</domain>
570
- <domain from="684" to="722" confidence="1.6E-8">WD40</domain>
571
- <domain from="726" to="764" confidence="6.0E-9">WD40</domain>
572
- <domain from="827" to="865" confidence="6.9E-10">WD40</domain>
573
- <domain from="868" to="906" confidence="1.2E-6">WD40</domain>
574
- <domain from="910" to="950" confidence="0.0080">WD40</domain>
575
- <domain from="954" to="994" confidence="0.0016">WD40</domain>
576
- <domain from="999" to="1037" confidence="4.9E-6">WD40</domain>
577
- <domain from="1042" to="1080" confidence="6.3E-8">WD40</domain>
578
- <domain from="1100" to="1138" confidence="1.9E-8">WD40</domain>
579
- <domain from="1142" to="1178" confidence="1.4">WD40</domain>
580
- <domain from="1577" to="1615" confidence="4.3E-4">WD40</domain>
581
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582
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583
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584
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585
- <clade>
586
- <name>19_NEMVE</name>
587
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588
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589
- <code>NEMVE</code>
590
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591
- <sequence>
592
- <domain_architecture length="1649">
593
- <domain from="99" to="174" confidence="4.6E-7">DED</domain>
594
- <domain from="181" to="503" confidence="8.0E-13">NB-ARC</domain>
595
- <domain from="696" to="734" confidence="1.4E-8">WD40</domain>
596
- <domain from="738" to="776" confidence="2.9E-9">WD40</domain>
597
- <domain from="780" to="818" confidence="3.8E-10">WD40</domain>
598
- <domain from="822" to="860" confidence="6.4E-9">WD40</domain>
599
- <domain from="864" to="902" confidence="2.1E-10">WD40</domain>
600
- <domain from="906" to="944" confidence="1.3E-8">WD40</domain>
601
- <domain from="948" to="986" confidence="1.2E-8">WD40</domain>
602
- <domain from="990" to="1028" confidence="9.4E-8">WD40</domain>
603
- <domain from="1032" to="1070" confidence="6.0E-8">WD40</domain>
604
- <domain from="1074" to="1112" confidence="2.6E-4">WD40</domain>
605
- <domain from="1364" to="1597" confidence="1.9">SGL</domain>
606
- <domain from="1442" to="1480" confidence="9.7E-7">WD40</domain>
607
- <domain from="1527" to="1565" confidence="1.2">WD40</domain>
608
- <domain from="1568" to="1606" confidence="1.1E-6">WD40</domain>
609
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610
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611
- </clade>
612
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613
- </clade>
614
- <clade>
615
- <branch_length>0.43438</branch_length>
616
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617
- <clade>
618
- <branch_length>0.92214</branch_length>
619
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620
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621
- <name>37_BRAFL</name>
622
- <branch_length>0.21133</branch_length>
623
- <taxonomy>
624
- <code>BRAFL</code>
625
- </taxonomy>
626
- <sequence>
627
- <domain_architecture length="1793">
628
- <domain from="6" to="89" confidence="9.6E-13">CARD</domain>
629
- <domain from="118" to="202" confidence="4.5E-9">CARD</domain>
630
- <domain from="206" to="491" confidence="0.0011">NB-ARC</domain>
631
- <domain from="238" to="388" confidence="0.0043">NACHT</domain>
632
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633
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634
- </clade>
635
- <clade>
636
- <name>36_BRAFL</name>
637
- <branch_length>0.16225</branch_length>
638
- <taxonomy>
639
- <code>BRAFL</code>
640
- </taxonomy>
641
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642
- <domain_architecture length="918">
643
- <domain from="9" to="93" confidence="1.6E-9">CARD</domain>
644
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645
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646
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647
- </clade>
648
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649
- <clade>
650
- <name>33_BRAFL</name>
651
- <branch_length>0.8363</branch_length>
652
- <taxonomy>
653
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654
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655
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656
- <domain_architecture length="1212">
657
- <domain from="5" to="87" confidence="4.7E-12">Death</domain>
658
- <domain from="154" to="465" confidence="2.0E-6">NB-ARC</domain>
659
- </domain_architecture>
660
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661
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662
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663
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664
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665
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666
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