bio 1.5.2 → 1.6.0.pre.20181210

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Files changed (93) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +12 -11
  3. data/ChangeLog +14 -3106
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -1
  5. data/KNOWN_ISSUES.rdoc +0 -5
  6. data/README.rdoc +11 -18
  7. data/RELEASE_NOTES.rdoc +34 -291
  8. data/Rakefile +13 -9
  9. data/appveyor.yml +21 -0
  10. data/bioruby.gemspec +7 -78
  11. data/bioruby.gemspec.erb +8 -27
  12. data/doc/ChangeLog-1.5.0 +2919 -0
  13. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  14. data/doc/Tutorial.rd +6 -108
  15. data/doc/Tutorial.rd.html +19 -98
  16. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  17. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  18. data/gemfiles/Gemfile.travis-rbx +0 -1
  19. data/gemfiles/Gemfile.travis-ruby1.8 +4 -4
  20. data/gemfiles/Gemfile.travis-ruby1.9 +0 -1
  21. data/gemfiles/prepare-gemspec.rb +4 -0
  22. data/lib/bio.rb +0 -10
  23. data/lib/bio/data/codontable.rb +99 -3
  24. data/lib/bio/io/togows.rb +5 -5
  25. data/lib/bio/version.rb +6 -8
  26. data/sample/test_restriction_enzyme_long.rb +1 -1
  27. data/test/unit/bio/data/test_codontable.rb +3 -0
  28. metadata +11 -77
  29. data/bin/bioruby +0 -47
  30. data/bin/br_biofetch.rb +0 -71
  31. data/bin/br_bioflat.rb +0 -293
  32. data/bin/br_biogetseq.rb +0 -45
  33. data/bin/br_pmfetch.rb +0 -422
  34. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  35. data/lib/bio/db/biosql/sequence.rb +0 -444
  36. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  37. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  38. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  39. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  40. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  41. data/lib/bio/io/biosql/biosql.rb +0 -39
  42. data/lib/bio/io/biosql/config/database.yml +0 -21
  43. data/lib/bio/io/sql.rb +0 -79
  44. data/lib/bio/shell.rb +0 -44
  45. data/lib/bio/shell/core.rb +0 -578
  46. data/lib/bio/shell/demo.rb +0 -146
  47. data/lib/bio/shell/interface.rb +0 -217
  48. data/lib/bio/shell/irb.rb +0 -94
  49. data/lib/bio/shell/object.rb +0 -71
  50. data/lib/bio/shell/plugin/blast.rb +0 -42
  51. data/lib/bio/shell/plugin/codon.rb +0 -218
  52. data/lib/bio/shell/plugin/das.rb +0 -58
  53. data/lib/bio/shell/plugin/emboss.rb +0 -23
  54. data/lib/bio/shell/plugin/entry.rb +0 -137
  55. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  56. data/lib/bio/shell/plugin/midi.rb +0 -430
  57. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  58. data/lib/bio/shell/plugin/obda.rb +0 -45
  59. data/lib/bio/shell/plugin/psort.rb +0 -56
  60. data/lib/bio/shell/plugin/seq.rb +0 -248
  61. data/lib/bio/shell/plugin/togows.rb +0 -40
  62. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  63. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  64. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  65. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  66. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  67. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  68. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  69. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  70. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  71. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  72. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  73. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  74. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  75. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  76. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  77. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  78. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  79. data/lib/bio/shell/script.rb +0 -25
  80. data/lib/bio/shell/setup.rb +0 -108
  81. data/lib/bio/shell/web.rb +0 -102
  82. data/sample/test_phyloxml_big.rb +0 -205
  83. data/test/data/phyloxml/apaf.xml +0 -666
  84. data/test/data/phyloxml/bcl_2.xml +0 -2097
  85. data/test/data/phyloxml/made_up.xml +0 -144
  86. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  87. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  88. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  89. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  90. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  91. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  92. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  93. data/test/unit/bio/test_shell.rb +0 -20
data/sample/test_phyloxml_big.rb DELETED
@@ -1,205 +0,0 @@
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- #
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- # = sample/test_phyloxml_big.rb - Tests for Bio::PhyloXML. Testing very big files.
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- #
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- # Copyright:: Copyright (C) 2009
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- # Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
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- # Naohisa Goto <ng@bioruby.org>
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- # License:: The Ruby License
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- #
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-
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- # libraries needed for the tests
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- require 'libxml'
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- require 'pathname'
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- require 'test/unit'
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- require 'digest/sha1'
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-
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- require 'bio/command'
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- require 'bio/db/phyloxml/phyloxml_parser'
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- require 'bio/db/phyloxml/phyloxml_writer'
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-
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- PhyloXMLBigDataPath = ARGV.shift
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-
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- if !PhyloXMLBigDataPath then
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- exit_code = 0
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- elsif !File.directory?(PhyloXMLBigDataPath) then
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- exit_code = 1
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- else
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- exit_code = false
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- end
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-
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- if exit_code then
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- puts "Usage: #{$0} path_to_data (test options...)"
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- puts ""
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- puts "Requirements:"
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- puts " - Write permission to the path_to_data"
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- puts " - Internet connection for downloading test data"
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- puts " - unzip command to extract downloaded test data"
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- puts ""
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- puts "You may want to run Ruby with -rubygems and -I<path_to_bioruby_lib>."
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- puts ""
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- puts "Example of usage using /tmp:"
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- puts " $ mkdir /tmp/phyloxml"
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- puts " $ ruby -rubygems -I lib #{$0} /tmp/phyloxml -v"
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- puts ""
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- exit(exit_code)
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- end
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-
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- module TestPhyloXMLBigData
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-
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- module_function
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-
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- def metazoa_xml
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- #puts "Metazoa 30MB"
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- filename = 'ncbi_taxonomy_metazoa.xml'
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- uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_metazoa.xml.zip"
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- download_and_unzip_if_not_found(filename, uri, "1M", "33M")
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- end
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-
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- def metazoa_test_xml
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- #puts "writing Metazoa 30MB"
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- File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_metazoa.xml'
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- end
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-
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- def metazoa_roundtrip_xml
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- #puts "writing Metazoa 30MB roundtrip"
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- File.join PhyloXMLBigDataPath, 'roundtrip_test_ncbi_taxonomy_metazoa.xml'
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- end
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-
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- def mollusca_xml
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- #puts "Mollusca 1.5MB"
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- filename = 'ncbi_taxonomy_mollusca.xml'
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- uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_mollusca.xml.zip"
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- download_and_unzip_if_not_found(filename, uri, "67K", "1.5M")
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- end
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-
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- def mollusca_test_xml
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- #puts "Writing Mollusca 1.5MB"
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- File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_mollusca.xml'
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- end
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-
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- def mollusca_roundtrip_xml
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- #puts "Writing Mollusca 1.5MB roundtrip"
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- File.join PhyloXMLBigDataPath, 'roundtrip_test_ncbi_taxonomy_mollusca.xml'
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- end
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-
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- def life_xml
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- #Right now this file is not compatible with xsd 1.10
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- filename = 'tol_life_on_earth_1.xml'
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- uri = "http://www.phylosoft.org/archaeopteryx/examples/data/tol_life_on_earth_1.xml.zip"
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-
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- download_and_unzip_if_not_found(filename, uri, '10M', '45M')
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- end
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-
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- def life_test_xml
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- File.join PhyloXMLBigDataPath, 'writer_test_tol_life_on_earth_1.xml'
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- end
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-
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- def life_roundtrip_xml
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- File.join PhyloXMLBigDataPath, 'roundtrip_test_tol_life_on_earth_1.xml'
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- end
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-
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- def unzip_file(file, target_dir)
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- flag = system('unzip', "#{file}.zip", "-d", target_dir)
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- unless flag then
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- raise "Failed to unzip #{file}.zip"
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- end
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- file
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- end
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-
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- def download_and_unzip_if_not_found(basename, uri, zipsize, origsize)
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- file = File.join PhyloXMLBigDataPath, basename
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- return file if File.exists?(file)
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-
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- if File.exists?("#{file}.zip")
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- unzip_file(file, PhyloXMLBigDataPath)
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- return file
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- end
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-
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- puts "File #{basename} does not exist. Do you want to download it? (If yes, ~#{zipsize}B zip file will be downloaded and extracted (to #{origsize}B), if no, the test will be skipped.) y/n?"
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- res = gets
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- if res.to_s.chomp.downcase == "y"
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- File.open("#{file}.zip", "wb") do |f|
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- f.write(Bio::Command.read_uri(uri))
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- end
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- puts "File downloaded."
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- self.unzip_file(file, PhyloXMLBigDataPath)
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- return file
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- else
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- return nil
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- #return File.join PHYLOXML_TEST_DATA, "#{basename}.stub"
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- end
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- end
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-
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- end #end module TestPhyloXMLBigData
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-
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- module Bio
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-
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- class TestPhyloXMLBig < Test::Unit::TestCase
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-
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- def do_test_next_tree(readfilename)
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- raise "the test is skipped" unless readfilename
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- filesizeMB = File.size(readfilename) / 1048576.0
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- printf "Reading %s (%2.1f MB)\n", readfilename, filesizeMB
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-
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- begin
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- phyloxml = Bio::PhyloXML::Parser.open(readfilename)
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- rescue NoMethodError
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- phyloxml = Bio::PhyloXML::Parser.new(readfilename)
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- end
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- tree = nil
150
- assert_nothing_raised {
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- tree = phyloxml.next_tree
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- }
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- tree
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- end
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- private :do_test_next_tree
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-
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- def do_test_write(tree, writefilename)
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- printf "Writing to %s\n", writefilename
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- writer = Bio::PhyloXML::Writer.new(writefilename)
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- assert_nothing_raised {
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- writer.write(tree)
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- }
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-
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- # checks file size and sha1sum
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- str = File.open(writefilename, 'rb') { |f| f.read }
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- sha1 = Digest::SHA1.hexdigest(str)
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- puts "Wrote #{str.length} bytes."
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- puts "sha1: #{sha1}"
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- end
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- private :do_test_write
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-
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- def test_mollusca
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- tree = do_test_next_tree(TestPhyloXMLBigData.mollusca_xml)
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- do_test_write(tree, TestPhyloXMLBigData.mollusca_test_xml)
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-
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- tree2 = do_test_next_tree(TestPhyloXMLBigData.mollusca_test_xml)
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- do_test_write(tree2, TestPhyloXMLBigData.mollusca_roundtrip_xml)
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- end
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-
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- def test_metazoa
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- tree = do_test_next_tree(TestPhyloXMLBigData.metazoa_xml)
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- do_test_write(tree, TestPhyloXMLBigData.metazoa_test_xml)
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-
184
- tree2 = do_test_next_tree(TestPhyloXMLBigData.metazoa_test_xml)
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- do_test_write(tree2, TestPhyloXMLBigData.metazoa_roundtrip_xml)
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- end
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-
188
- if false
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- # Disabled because of the error.
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- # LibXML::XML::Error: Fatal error: Input is not proper UTF-8,
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- # indicate encoding !
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- # Bytes: 0xE9 0x6B 0x65 0x73 at tol_life_on_earth_1.xml:132170.
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- #
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- def test_life
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- tree = do_test_next_tree(TestPhyloXMLBigData.life_xml)
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- do_test_write(tree, TestPhyloXMLBigData.life_test_xml)
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-
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- tree2 = do_test_next_tree(TestPhyloXMLBigData.life_test_xml)
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- do_test_write(tree2, TestPhyloXMLBigData.life_roundtrip_xml)
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- end
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- end #if false
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-
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- end
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-
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- end
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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- <clade>
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- <branch_length>0.18105</branch_length>
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- <confidence type="unknown">89.0</confidence>
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- <clade>
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- <branch_length>0.07466</branch_length>
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- <confidence type="unknown">32.0</confidence>
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- <clade>
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- <branch_length>0.26168</branch_length>
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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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- <branch_length>0.28901</branch_length>
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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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- <domain from="639" to="677" confidence="2.5E-11">WD40</domain>
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- <domain from="681" to="721" confidence="1.8E-7">WD40</domain>
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- <domain from="725" to="763" confidence="9.4E-13">WD40</domain>
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- <domain from="889" to="927" confidence="1.1E-6">WD40</domain>
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- <domain from="971" to="1009" confidence="1.7E-7">WD40</domain>
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- <domain from="1013" to="1051" confidence="1.9E-7">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>11_CHICK</name>
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- <branch_length>0.15226</branch_length>
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- <taxonomy>
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- <code>CHICK</code>
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- </taxonomy>
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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="603" to="641" confidence="1.6E-4">WD40</domain>
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- <domain from="645" to="683" confidence="8.2E-11">WD40</domain>
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- <domain from="687" to="727" confidence="6.2E-10">WD40</domain>
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- <domain from="731" to="769" confidence="1.8E-11">WD40</domain>
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- <domain from="828" to="866" confidence="1.8">WD40</domain>
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- <domain from="993" to="1030" confidence="2.9E-4">WD40</domain>
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- <domain from="1034" to="1072" confidence="1.7E-8">WD40</domain>
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- <domain from="1076" to="1114" confidence="7.5E-9">WD40</domain>
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- <domain from="1127" to="1163" confidence="0.044">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>16_XENLA</name>
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- <branch_length>0.4409</branch_length>
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- <taxonomy>
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- <code>XENLA</code>
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- </taxonomy>
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- <sequence>
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- <domain_architecture length="1362">
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- <domain from="6" to="90" confidence="4.0E-20">CARD</domain>
128
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129
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130
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131
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142
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143
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144
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145
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146
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147
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148
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149
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150
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151
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152
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156
- <domain from="8" to="92" confidence="4.6E-24">CARD</domain>
157
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158
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159
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160
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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175
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176
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177
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178
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179
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180
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181
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182
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183
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185
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186
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187
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188
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189
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190
- <code>BRARE</code>
191
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192
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193
- <domain_architecture length="1260">
194
- <domain from="6" to="90" confidence="3.9E-23">CARD</domain>
195
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196
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197
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198
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199
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206
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208
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209
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210
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211
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212
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213
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214
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215
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216
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217
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218
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219
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221
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222
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223
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224
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225
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232
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233
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234
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235
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236
- <name>18_NEMVE</name>
237
- <branch_length>0.38014</branch_length>
238
- <taxonomy>
239
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240
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241
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242
- <domain_architecture length="1290">
243
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244
- <domain from="117" to="200" confidence="5.4E-14">CARD</domain>
245
- <domain from="216" to="517" confidence="1.5E-50">NB-ARC</domain>
246
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247
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252
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254
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255
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256
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- </clade>
258
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259
- <clade>
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
- <taxonomy>
304
- <code>STRPU</code>
305
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306
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307
- <domain_architecture length="1947">
308
- <domain from="143" to="227" confidence="7.4E-5">Death</domain>
309
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310
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311
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312
- <domain from="1741" to="1836" confidence="2.0">Adeno_VII</domain>
313
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314
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315
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316
- </clade>
317
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318
- <clade>
319
- <branch_length>1.31498</branch_length>
320
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321
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322
- <name>CED4_CAEEL</name>
323
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324
- <taxonomy>
325
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326
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327
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328
- <domain_architecture length="714">
329
- <domain from="7" to="90" confidence="9.2E-14">CARD</domain>
330
- <domain from="116" to="442" confidence="5.8E-151">NB-ARC</domain>
331
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332
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333
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334
- <clade>
335
- <name>31_CAEBR</name>
336
- <branch_length>0.04777</branch_length>
337
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338
- <code>CAEBR</code>
339
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340
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341
- <domain_architecture length="554">
342
- <domain from="1" to="75" confidence="0.0046">CARD</domain>
343
- <domain from="101" to="427" confidence="2.1E-123">NB-ARC</domain>
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
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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
- <domain_architecture length="535">
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
- <code>DROME</code>
375
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376
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377
- <domain_architecture length="1421">
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
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384
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385
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386
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387
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388
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389
- <sequence>
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
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398
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399
- <taxonomy>
400
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401
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402
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403
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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
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410
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411
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412
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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
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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
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430
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431
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432
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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
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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
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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
- </taxonomy>
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
- <clade>
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
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484
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485
- <domain from="698" to="731" confidence="4.2E-5">TPR_2</domain>
486
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487
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488
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489
- <clade>
490
- <name>21_NEMVE</name>
491
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492
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493
- <code>NEMVE</code>
494
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495
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496
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497
- <domain from="234" to="317" confidence="2.3E-14">CARD</domain>
498
- <domain from="238" to="318" confidence="0.5">Death</domain>
499
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500
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501
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502
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503
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505
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506
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507
- <clade>
508
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509
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510
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511
- <code>BRAFL</code>
512
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514
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515
- <domain from="5" to="321" confidence="5.0E-5">NB-ARC</domain>
516
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517
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518
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519
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520
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521
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522
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523
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524
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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540
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541
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542
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543
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544
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545
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546
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547
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552
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553
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554
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555
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556
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557
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558
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559
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560
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561
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562
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564
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565
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566
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567
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568
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569
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570
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571
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572
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573
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574
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575
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576
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577
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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
- </sequence>
583
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584
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585
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586
- <name>19_NEMVE</name>
587
- <branch_length>0.57144</branch_length>
588
- <taxonomy>
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
- </clade>
613
- </clade>
614
- <clade>
615
- <branch_length>0.43438</branch_length>
616
- <confidence type="unknown">92.0</confidence>
617
- <clade>
618
- <branch_length>0.92214</branch_length>
619
- <confidence type="unknown">100.0</confidence>
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
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635
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636
- <name>36_BRAFL</name>
637
- <branch_length>0.16225</branch_length>
638
- <taxonomy>
639
- <code>BRAFL</code>
640
- </taxonomy>
641
- <sequence>
642
- <domain_architecture length="918">
643
- <domain from="9" to="93" confidence="1.6E-9">CARD</domain>
644
- <domain from="98" to="403" confidence="0.0019">NB-ARC</domain>
645
- </domain_architecture>
646
- </sequence>
647
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648
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649
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650
- <name>33_BRAFL</name>
651
- <branch_length>0.8363</branch_length>
652
- <taxonomy>
653
- <code>BRAFL</code>
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
- </clade>
664
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665
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666
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