bio 1.5.2 → 1.6.0.pre.20181210

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 @@
1
- #
2
- # = sample/test_phyloxml_big.rb - Tests for Bio::PhyloXML. Testing very big files.
3
- #
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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
8
- #
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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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-
20
- PhyloXMLBigDataPath = ARGV.shift
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-
22
- if !PhyloXMLBigDataPath then
23
- exit_code = 0
24
- elsif !File.directory?(PhyloXMLBigDataPath) then
25
- exit_code = 1
26
- else
27
- exit_code = false
28
- end
29
-
30
- if exit_code then
31
- puts "Usage: #{$0} path_to_data (test options...)"
32
- puts ""
33
- puts "Requirements:"
34
- puts " - Write permission to the path_to_data"
35
- 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:"
41
- puts " $ mkdir /tmp/phyloxml"
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- puts " $ ruby -rubygems -I lib #{$0} /tmp/phyloxml -v"
43
- puts ""
44
- exit(exit_code)
45
- end
46
-
47
- module TestPhyloXMLBigData
48
-
49
- module_function
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-
51
- def metazoa_xml
52
- #puts "Metazoa 30MB"
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- filename = 'ncbi_taxonomy_metazoa.xml'
54
- uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_metazoa.xml.zip"
55
- download_and_unzip_if_not_found(filename, uri, "1M", "33M")
56
- end
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-
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- def metazoa_test_xml
59
- #puts "writing Metazoa 30MB"
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- File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_metazoa.xml'
61
- 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"
70
- filename = 'ncbi_taxonomy_mollusca.xml'
71
- 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")
73
- end
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-
75
- def mollusca_test_xml
76
- #puts "Writing Mollusca 1.5MB"
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- File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_mollusca.xml'
78
- end
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-
80
- def mollusca_roundtrip_xml
81
- #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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-
85
- def life_xml
86
- #Right now this file is not compatible with xsd 1.10
87
- filename = 'tol_life_on_earth_1.xml'
88
- uri = "http://www.phylosoft.org/archaeopteryx/examples/data/tol_life_on_earth_1.xml.zip"
89
-
90
- download_and_unzip_if_not_found(filename, uri, '10M', '45M')
91
- end
92
-
93
- def life_test_xml
94
- File.join PhyloXMLBigDataPath, 'writer_test_tol_life_on_earth_1.xml'
95
- end
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-
97
- def life_roundtrip_xml
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- File.join PhyloXMLBigDataPath, 'roundtrip_test_tol_life_on_earth_1.xml'
99
- end
100
-
101
- def unzip_file(file, target_dir)
102
- flag = system('unzip', "#{file}.zip", "-d", target_dir)
103
- unless flag then
104
- raise "Failed to unzip #{file}.zip"
105
- end
106
- file
107
- end
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-
109
- def download_and_unzip_if_not_found(basename, uri, zipsize, origsize)
110
- file = File.join PhyloXMLBigDataPath, basename
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- return file if File.exists?(file)
112
-
113
- if File.exists?("#{file}.zip")
114
- unzip_file(file, PhyloXMLBigDataPath)
115
- return file
116
- end
117
-
118
- 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?"
119
- res = gets
120
- if res.to_s.chomp.downcase == "y"
121
- File.open("#{file}.zip", "wb") do |f|
122
- f.write(Bio::Command.read_uri(uri))
123
- end
124
- puts "File downloaded."
125
- self.unzip_file(file, PhyloXMLBigDataPath)
126
- return file
127
- else
128
- return nil
129
- #return File.join PHYLOXML_TEST_DATA, "#{basename}.stub"
130
- end
131
- end
132
-
133
- end #end module TestPhyloXMLBigData
134
-
135
- module Bio
136
-
137
- class TestPhyloXMLBig < Test::Unit::TestCase
138
-
139
- def do_test_next_tree(readfilename)
140
- raise "the test is skipped" unless readfilename
141
- filesizeMB = File.size(readfilename) / 1048576.0
142
- printf "Reading %s (%2.1f MB)\n", readfilename, filesizeMB
143
-
144
- begin
145
- phyloxml = Bio::PhyloXML::Parser.open(readfilename)
146
- rescue NoMethodError
147
- phyloxml = Bio::PhyloXML::Parser.new(readfilename)
148
- end
149
- tree = nil
150
- assert_nothing_raised {
151
- tree = phyloxml.next_tree
152
- }
153
- tree
154
- end
155
- private :do_test_next_tree
156
-
157
- def do_test_write(tree, writefilename)
158
- printf "Writing to %s\n", writefilename
159
- writer = Bio::PhyloXML::Writer.new(writefilename)
160
- assert_nothing_raised {
161
- writer.write(tree)
162
- }
163
-
164
- # checks file size and sha1sum
165
- str = File.open(writefilename, 'rb') { |f| f.read }
166
- sha1 = Digest::SHA1.hexdigest(str)
167
- puts "Wrote #{str.length} bytes."
168
- puts "sha1: #{sha1}"
169
- end
170
- private :do_test_write
171
-
172
- def test_mollusca
173
- tree = do_test_next_tree(TestPhyloXMLBigData.mollusca_xml)
174
- do_test_write(tree, TestPhyloXMLBigData.mollusca_test_xml)
175
-
176
- tree2 = do_test_next_tree(TestPhyloXMLBigData.mollusca_test_xml)
177
- do_test_write(tree2, TestPhyloXMLBigData.mollusca_roundtrip_xml)
178
- end
179
-
180
- def test_metazoa
181
- tree = do_test_next_tree(TestPhyloXMLBigData.metazoa_xml)
182
- do_test_write(tree, TestPhyloXMLBigData.metazoa_test_xml)
183
-
184
- tree2 = do_test_next_tree(TestPhyloXMLBigData.metazoa_test_xml)
185
- do_test_write(tree2, TestPhyloXMLBigData.metazoa_roundtrip_xml)
186
- end
187
-
188
- if false
189
- # Disabled because of the error.
190
- # LibXML::XML::Error: Fatal error: Input is not proper UTF-8,
191
- # indicate encoding !
192
- # Bytes: 0xE9 0x6B 0x65 0x73 at tol_life_on_earth_1.xml:132170.
193
- #
194
- def test_life
195
- tree = do_test_next_tree(TestPhyloXMLBigData.life_xml)
196
- do_test_write(tree, TestPhyloXMLBigData.life_test_xml)
197
-
198
- tree2 = do_test_next_tree(TestPhyloXMLBigData.life_test_xml)
199
- do_test_write(tree2, TestPhyloXMLBigData.life_roundtrip_xml)
200
- end
201
- end #if false
202
-
203
- 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"?>
2
- <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">
3
- <phylogeny rooted="true">
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- <clade>
5
- <clade>
6
- <branch_length>0.18105</branch_length>
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- <confidence type="unknown">89.0</confidence>
8
- <clade>
9
- <branch_length>0.07466</branch_length>
10
- <confidence type="unknown">32.0</confidence>
11
- <clade>
12
- <branch_length>0.26168</branch_length>
13
- <confidence type="unknown">100.0</confidence>
14
- <clade>
15
- <branch_length>0.22058</branch_length>
16
- <confidence type="unknown">89.0</confidence>
17
- <clade>
18
- <branch_length>0.28901</branch_length>
19
- <confidence type="unknown">100.0</confidence>
20
- <clade>
21
- <branch_length>0.06584</branch_length>
22
- <confidence type="unknown">100.0</confidence>
23
- <clade>
24
- <branch_length>0.02309</branch_length>
25
- <confidence type="unknown">43.0</confidence>
26
- <clade>
27
- <branch_length>0.0746</branch_length>
28
- <confidence type="unknown">100.0</confidence>
29
- <clade>
30
- <branch_length>0.02365</branch_length>
31
- <confidence type="unknown">88.0</confidence>
32
- <clade>
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- <name>22_MOUSE</name>
34
- <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">
40
- <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>
56
- <branch_length>0.01825</branch_length>
57
- <taxonomy>
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- <code>HUMAN</code>
59
- </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>
74
- </clade>
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- <clade>
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- <name>12_CANFA</name>
77
- <branch_length>0.04683</branch_length>
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- <taxonomy>
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- <code>CANFA</code>
80
- </taxonomy>
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- <sequence>
82
- <domain_architecture length="1153">
83
- <domain from="6" to="90" confidence="4.5E-22">CARD</domain>
84
- <domain from="110" to="415" confidence="4.0E-119">NB-ARC</domain>
85
- <domain from="597" to="635" confidence="3.9E-5">WD40</domain>
86
- <domain from="639" to="677" confidence="2.5E-11">WD40</domain>
87
- <domain from="681" to="721" confidence="1.8E-7">WD40</domain>
88
- <domain from="725" to="763" confidence="9.4E-13">WD40</domain>
89
- <domain from="889" to="927" confidence="1.1E-6">WD40</domain>
90
- <domain from="971" to="1009" confidence="1.7E-7">WD40</domain>
91
- <domain from="1013" to="1051" confidence="1.9E-7">WD40</domain>
92
- </domain_architecture>
93
- </sequence>
94
- </clade>
95
- </clade>
96
- <clade>
97
- <name>11_CHICK</name>
98
- <branch_length>0.15226</branch_length>
99
- <taxonomy>
100
- <code>CHICK</code>
101
- </taxonomy>
102
- <sequence>
103
- <domain_architecture length="1207">
104
- <domain from="6" to="90" confidence="3.6E-21">CARD</domain>
105
- <domain from="109" to="414" confidence="3.6E-109">NB-ARC</domain>
106
- <domain from="603" to="641" confidence="1.6E-4">WD40</domain>
107
- <domain from="645" to="683" confidence="8.2E-11">WD40</domain>
108
- <domain from="687" to="727" confidence="6.2E-10">WD40</domain>
109
- <domain from="731" to="769" confidence="1.8E-11">WD40</domain>
110
- <domain from="828" to="866" confidence="1.8">WD40</domain>
111
- <domain from="993" to="1030" confidence="2.9E-4">WD40</domain>
112
- <domain from="1034" to="1072" confidence="1.7E-8">WD40</domain>
113
- <domain from="1076" to="1114" confidence="7.5E-9">WD40</domain>
114
- <domain from="1127" to="1163" confidence="0.044">WD40</domain>
115
- </domain_architecture>
116
- </sequence>
117
- </clade>
118
- </clade>
119
- <clade>
120
- <name>16_XENLA</name>
121
- <branch_length>0.4409</branch_length>
122
- <taxonomy>
123
- <code>XENLA</code>
124
- </taxonomy>
125
- <sequence>
126
- <domain_architecture length="1362">
127
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212
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213
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214
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236
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237
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243
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244
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260
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262
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266
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278
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279
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283
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284
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287
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288
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289
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290
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292
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293
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304
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308
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312
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315
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316
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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
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330
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331
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332
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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
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343
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344
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348
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349
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350
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354
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355
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356
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359
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360
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361
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364
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366
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367
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368
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372
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373
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374
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375
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376
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377
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378
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379
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380
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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
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390
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391
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392
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393
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397
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398
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399
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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
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406
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407
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408
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410
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413
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414
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417
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418
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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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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
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434
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435
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436
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437
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438
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439
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440
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441
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442
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443
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444
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445
- <taxonomy>
446
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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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455
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456
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457
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458
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459
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460
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461
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462
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464
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465
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466
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468
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469
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470
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471
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472
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473
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474
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475
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476
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477
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478
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479
- <domain_architecture length="786">
480
- <domain from="8" to="91" confidence="1.7E-17">DED</domain>
481
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482
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483
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484
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485
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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
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494
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495
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496
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497
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498
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499
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500
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501
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502
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508
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511
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515
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519
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522
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523
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527
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528
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529
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530
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532
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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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543
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544
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545
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555
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556
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558
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561
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562
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564
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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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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
- </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
- </sequence>
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
- <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
- </clade>
648
- </clade>
649
- <clade>
650
- <name>33_BRAFL</name>
651
- <branch_length>0.8363</branch_length>
652
- <taxonomy>
653
- <code>BRAFL</code>
654
- </taxonomy>
655
- <sequence>
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
- </sequence>
661
- </clade>
662
- </clade>
663
- </clade>
664
- </clade>
665
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666
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