bio 1.5.1 → 2.0.2

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Files changed (128) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +35 -36
  3. data/ChangeLog +911 -2554
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
  5. data/KNOWN_ISSUES.rdoc +10 -13
  6. data/LEGAL +0 -10
  7. data/README.rdoc +40 -96
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +118 -234
  10. data/Rakefile +13 -43
  11. data/appveyor.yml +29 -0
  12. data/bioruby.gemspec +18 -81
  13. data/bioruby.gemspec.erb +8 -28
  14. data/doc/ChangeLog-1.5.0 +2919 -0
  15. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  16. data/doc/Tutorial.rd +6 -108
  17. data/doc/Tutorial.rd.html +19 -98
  18. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  19. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  20. data/gemfiles/Gemfile.travis-rbx +0 -3
  21. data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
  22. data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
  23. data/gemfiles/Gemfile.windows +6 -0
  24. data/gemfiles/prepare-gemspec.rb +4 -0
  25. data/lib/bio.rb +0 -10
  26. data/lib/bio/appl/blast/genomenet.rb +4 -4
  27. data/lib/bio/appl/blast/report.rb +40 -8
  28. data/lib/bio/appl/fasta/format10.rb +2 -1
  29. data/lib/bio/command.rb +10 -0
  30. data/lib/bio/data/codontable.rb +99 -3
  31. data/lib/bio/db/aaindex.rb +74 -5
  32. data/lib/bio/db/gff.rb +3 -1
  33. data/lib/bio/db/kegg/common.rb +14 -0
  34. data/lib/bio/db/kegg/genes.rb +26 -0
  35. data/lib/bio/db/kegg/pathway.rb +5 -11
  36. data/lib/bio/db/soft.rb +2 -2
  37. data/lib/bio/io/flatfile/autodetection.rb +5 -0
  38. data/lib/bio/io/togows.rb +5 -5
  39. data/lib/bio/map.rb +4 -4
  40. data/lib/bio/sequence/format.rb +1 -0
  41. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
  42. data/lib/bio/util/sirna.rb +2 -0
  43. data/lib/bio/version.rb +6 -8
  44. data/sample/color_scheme_aa.rb +82 -0
  45. data/sample/color_scheme_na.rb +5 -6
  46. data/sample/fastq2html.cwl +23 -0
  47. data/sample/fastq2html.rb +94 -0
  48. data/sample/fastq2html.testdata.yaml +5 -0
  49. data/sample/na2aa.cwl +23 -0
  50. data/sample/na2aa.rb +11 -25
  51. data/sample/na2aa.testdata.yaml +7 -0
  52. data/sample/rev_comp.cwl +23 -0
  53. data/sample/rev_comp.rb +20 -0
  54. data/sample/rev_comp.testdata.yaml +7 -0
  55. data/sample/test_restriction_enzyme_long.rb +1 -1
  56. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  57. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  58. data/test/unit/bio/data/test_codontable.rb +3 -0
  59. data/test/unit/bio/db/test_gff.rb +5 -0
  60. data/test/unit/bio/test_alignment.rb +2 -2
  61. metadata +20 -77
  62. data/bin/bioruby +0 -47
  63. data/bin/br_biofetch.rb +0 -71
  64. data/bin/br_bioflat.rb +0 -293
  65. data/bin/br_biogetseq.rb +0 -45
  66. data/bin/br_pmfetch.rb +0 -422
  67. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  68. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  69. data/lib/bio/db/biosql/sequence.rb +0 -444
  70. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  71. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  72. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  73. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  74. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  75. data/lib/bio/io/biosql/biosql.rb +0 -39
  76. data/lib/bio/io/biosql/config/database.yml +0 -21
  77. data/lib/bio/io/sql.rb +0 -79
  78. data/lib/bio/shell.rb +0 -44
  79. data/lib/bio/shell/core.rb +0 -578
  80. data/lib/bio/shell/demo.rb +0 -146
  81. data/lib/bio/shell/interface.rb +0 -217
  82. data/lib/bio/shell/irb.rb +0 -94
  83. data/lib/bio/shell/object.rb +0 -71
  84. data/lib/bio/shell/plugin/blast.rb +0 -42
  85. data/lib/bio/shell/plugin/codon.rb +0 -218
  86. data/lib/bio/shell/plugin/das.rb +0 -58
  87. data/lib/bio/shell/plugin/emboss.rb +0 -23
  88. data/lib/bio/shell/plugin/entry.rb +0 -137
  89. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  90. data/lib/bio/shell/plugin/midi.rb +0 -430
  91. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  92. data/lib/bio/shell/plugin/obda.rb +0 -45
  93. data/lib/bio/shell/plugin/psort.rb +0 -56
  94. data/lib/bio/shell/plugin/seq.rb +0 -248
  95. data/lib/bio/shell/plugin/togows.rb +0 -40
  96. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  97. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  98. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  99. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  100. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  101. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  102. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  103. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  104. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  105. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  106. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  107. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  108. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  109. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  110. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  111. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  112. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  113. data/lib/bio/shell/script.rb +0 -25
  114. data/lib/bio/shell/setup.rb +0 -108
  115. data/lib/bio/shell/web.rb +0 -102
  116. data/sample/test_phyloxml_big.rb +0 -205
  117. data/setup.rb +0 -1600
  118. data/test/data/phyloxml/apaf.xml +0 -666
  119. data/test/data/phyloxml/bcl_2.xml +0 -2097
  120. data/test/data/phyloxml/made_up.xml +0 -144
  121. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  122. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  123. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  124. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  125. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  126. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  127. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  128. data/test/unit/bio/test_shell.rb +0 -20
data/test/data/phyloxml/made_up.xml DELETED
@@ -1,144 +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" rerootable="false" branch_length_unit="1">
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- <name>testing confidence</name>
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- <confidence type="bootstrap">89</confidence>
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- <confidence type="probability">0.71</confidence>
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- <clade>
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- <name>b</name>
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- <width>0.2</width>
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- <clade>
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- <name>c</name>
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- <confidence type="probability">0.9</confidence>
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- <confidence type="probability">0.71</confidence>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>testing polygon</name>
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- <clade>
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- <clade>
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- <name>A</name>
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- <distribution>
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- <desc>Polygon from random points</desc>
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- <polygon>
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- <point geodetic_datum="WGS84" alt_unit="m">
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- <lat>47.481277</lat>
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- <long>8.769303</long>
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- <alt>472</alt>
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- </point>
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- <point geodetic_datum="WGS84">
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- <lat>35.155904</lat>
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- <long>136.915863</long>
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- <alt>10</alt>
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- </point>
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- <point geodetic_datum="WGS84">
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- <lat>47.376334</lat>
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- <long>8.548108</long>
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- <alt>452</alt>
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- </point>
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- </polygon>
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- <polygon>
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- <point geodetic_datum="WGS84">
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- <lat>40.481277</lat>
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- <long>8.769303</long>
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- <alt>42</alt>
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- </point>
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- <point geodetic_datum="WGS84">
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- <lat>25.155904</lat>
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- <long>136.915863</long>
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- <alt>10</alt>
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- </point>
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- <point geodetic_datum="WGS84">
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- <lat>47.376334</lat>
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- <long>7.548108</long>
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- <alt>452</alt>
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- </point>
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- </polygon>
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- </distribution>
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- </clade>
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- <clade>
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- <name>B</name>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>testing references</name>
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- <clade>
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- <clade>
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- <name>A</name>
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- <reference doi="10.1093/bioinformatics/btm619">
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- <desc>Phyutility: a phyloinformatics tool for trees, alignments and molecular data</desc>
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- </reference>
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- <reference doi="10.1186/1471-2105-9-S1-S23"></reference>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <clade>
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- <name>A</name>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>Example of domain. Taken from apaf.mxl</name>
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- <clade>
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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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- <synonym>murine</synonym>
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- <synonym>vermin</synonym>
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- </taxonomy>
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- <sequence>
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- <annotation>
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- <desc>alcohol dehydrogenase</desc>
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- <confidence type="probability">0.99</confidence>
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- <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m">1200</property>
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- </annotation>
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- <domain_architecture length="1249">
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- <domain from="6" to="90" confidence="7.0E-26" id="x">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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- </phylogeny>
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- <phylogeny rooted="true" rerootable="false">
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- <name>dollo_on_domains__cofilin_e1/o_tol_332</name>
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- <description>[Method: Dollo parsimony on domain presence/absence] [Date: 2008/08/20 18:23:46] [Cost: 4] [Gains: 2] [Losses: 2] [Unchanged: 1314] [Parameters: E-value: 0.1, Cutoff-scores-file: not-set, Max-overlap: 0, Engulfing-overlaps: not-allowed, Ignore-dufs: false]</description>
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- <confidence type="parsimony">4.0</confidence>
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- <clade>
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- <name>cellular_organisms</name>
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- <binary_characters type="parsimony inferred" gained_count="0" lost_count="0" present_count="0">
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- </binary_characters>
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- <clade>
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- <name>Neomura</name>
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- <binary_characters type="parsimony inferred" gained_count="0" lost_count="0" present_count="0">
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- </binary_characters>
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- <clade>
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- <name>Eukaryota</name>
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- <binary_characters type="parsimony inferred" gained_count="2" lost_count="0" present_count="2">
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- <gained>
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- <bc>Cofilin_ADF</bc>
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- <bc>Gelsolin</bc>
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- </gained>
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- <present>
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- <bc>Cofilin_ADF</bc>
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- <bc>Gelsolin</bc>
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- </present>
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- </binary_characters>
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- </clade>
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- </clade>
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- </clade>
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- </phylogeny>
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- </phyloxml>
data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml DELETED
@@ -1,65 +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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- <taxonomy>
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- <scientific_name>Mollusca</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Gastropoda</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Orthogastropoda</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Vetigastropoda</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Haliotoidea</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Haliotidae</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Sulculus</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Sulculus diversicolor</scientific_name>
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- </taxonomy>
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- </clade>
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- </clade>
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- </clade>
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- </clade>
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- </clade>
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- </clade>
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- <clade>
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- <taxonomy>
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- <scientific_name>Eogastropoda</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Docoglossa</scientific_name>
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- </taxonomy>
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- </clade>
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- </clade>
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- </clade>
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- <clade>
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- <taxonomy>
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- <scientific_name>Bivalvia</scientific_name>
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- </taxonomy>
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- <clade>
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- <taxonomy>
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- <scientific_name>Heteroconchia</scientific_name>
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- </taxonomy>
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- </clade>
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- </clade>
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- </clade>
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- </phylogeny>
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- </phyloxml>
data/test/data/phyloxml/phyloxml_examples.xml DELETED
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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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- <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
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- <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
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- <clade>
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- <clade branch_length="0.06">
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- <clade branch_length="0.102">
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- <name>A</name>
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- </clade>
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- <clade branch_length="0.23">
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- <name>B</name>
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- </clade>
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- </clade>
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- <clade branch_length="0.4">
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- <name>C</name>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
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- <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
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- <clade>
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- <clade>
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- <branch_length>0.06</branch_length>
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- <clade>
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- <name>A</name>
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- <branch_length>0.102</branch_length>
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- </clade>
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- <clade>
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- <name>B</name>
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- <branch_length>0.23</branch_length>
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- </clade>
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- </clade>
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- <clade>
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- <name>C</name>
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- <branch_length>0.4</branch_length>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>same example, with support of type "bootstrap"</name>
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- <clade>
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- <clade branch_length="0.06">
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- <name>AB</name>
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- <confidence type="bootstrap">89</confidence>
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- <clade branch_length="0.102">
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- <name>A</name>
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- </clade>
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- <clade branch_length="0.23">
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- <name>B</name>
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- </clade>
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- </clade>
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- <clade branch_length="0.4">
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- <name>C</name>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>same example, with species and sequence</name>
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- <clade>
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- <clade>
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- <name>AB</name>
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- <clade>
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- <name>A</name>
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- <taxonomy>
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- <scientific_name>E. coli</scientific_name>
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- <authority>J. G. Cooper, 1863</authority>
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- </taxonomy>
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- <sequence>
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- <annotation>
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- <desc>alcohol dehydrogenase</desc>
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- <confidence type="probability">0.99</confidence>
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- </annotation>
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- </sequence>
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- </clade>
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- <clade>
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- <name>B</name>
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- <taxonomy>
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- <scientific_name>B. subtilis</scientific_name>
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- </taxonomy>
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- <sequence>
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- <annotation>
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- <desc>alcohol dehydrogenase</desc>
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- <confidence type="probability">0.91</confidence>
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- </annotation>
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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>C</name>
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- <taxonomy>
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- <scientific_name>C. elegans</scientific_name>
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- </taxonomy>
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- <sequence>
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- <annotation>
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- <desc>alcohol dehydrogenase</desc>
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- <confidence type="probability">0.67</confidence>
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- </annotation>
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- </sequence>
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- </clade>
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- </clade>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>same example, with gene duplication information and sequence relationships</name>
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- <clade>
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- <events>
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- <speciations>1</speciations>
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- </events>
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- <clade>
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- <events>
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- <duplications>1</duplications>
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- </events>
114
- <clade>
115
- <taxonomy>
116
- <scientific_name>Bacillus subtilis</scientific_name>
117
- </taxonomy>
118
- <sequence id_source="x">
119
- <symbol>adhB</symbol>
120
- <accession source="ncbi">AAB80874</accession>
121
- <name>alcohol dehydrogenase</name>
122
- </sequence>
123
- </clade>
124
- <clade>
125
- <taxonomy>
126
- <scientific_name>Bacillus subtilis</scientific_name>
127
- </taxonomy>
128
- <sequence id_source="y">
129
- <symbol>gbsB</symbol>
130
- <accession source="ncbi">CAB15083</accession>
131
- <name>alcohol dehydrogenase</name>
132
- </sequence>
133
- </clade>
134
- </clade>
135
- <clade>
136
- <taxonomy>
137
- <scientific_name>Caenorhabditis elegans</scientific_name>
138
- </taxonomy>
139
- <sequence id_source="z">
140
- <symbol>ADHX</symbol>
141
- <accession source="ncbi">Q17335</accession>
142
- <name>alcohol dehydrogenase</name>
143
- <annotation ref="InterPro:IPR002085"/>
144
- </sequence>
145
- </clade>
146
- </clade>
147
- <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>
148
- <sequence_relation id_ref_0="x" id_ref_1="z" type="orthology"/>
149
- <sequence_relation id_ref_0="y" id_ref_1="z" type="orthology"/>
150
- </phylogeny>
151
- <phylogeny rooted="true">
152
- <name>similar example, with more detailed sequence data</name>
153
- <clade>
154
- <clade>
155
- <clade>
156
- <taxonomy>
157
- <id provider="NCBI">6645</id>
158
- <code>OCTVU</code>
159
- <scientific_name>Octopus vulgaris</scientific_name>
160
- </taxonomy>
161
- <sequence>
162
- <symbol>ADHX</symbol>
163
- <accession source="UniProtKB">P81431</accession>
164
- <name>Alcohol dehydrogenase class-3</name>
165
- <mol_seq is_aligned="true">TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>
166
- <annotation ref="EC:1.1.1.1"/>
167
- <annotation ref="GO:0004022"/>
168
- </sequence>
169
- </clade>
170
- <clade>
171
- <taxonomy>
172
- <id provider="NCBI">44689</id>
173
- <code>DICDI</code>
174
- <scientific_name>Dictyostelium discoideum</scientific_name>
175
- </taxonomy>
176
- <sequence>
177
- <symbol>RT4I1</symbol>
178
- <accession source="UniProtKB">Q54II4</accession>
179
- <name>Reticulon-4-interacting protein 1 homolog, mitochondrial precursor</name>
180
- <mol_seq is_aligned="true">MKGILLNGYGESLDLLEYKTDLPVPKPIKSQVLIKIHSTSINPLDNVMRK</mol_seq>
181
- <annotation ref="GO:0008270"/>
182
- <annotation ref="GO:0016491"/>
183
- </sequence>
184
- </clade>
185
- </clade>
186
- <clade>
187
- <taxonomy>
188
- <id provider="NCBI">1488</id>
189
- <code>CLOAB</code>
190
- <scientific_name>Clostridium acetobutylicum</scientific_name>
191
- </taxonomy>
192
- <sequence>
193
- <symbol>ADHB</symbol>
194
- <accession source="UniProtKB">Q04945</accession>
195
- <name>NADH-dependent butanol dehydrogenase B</name>
196
- <mol_seq is_aligned="true">MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK</mol_seq>
197
- <annotation ref="GO:0046872"/>
198
- <annotation ref="KEGG:Tetrachloroethene degradation"/>
199
- </sequence>
200
- </clade>
201
- </clade>
202
- </phylogeny>
203
- <phylogeny rooted="false">
204
- <name>network, node B is connected to TWO nodes: AB and C</name>
205
- <clade>
206
- <clade id_source="ab" branch_length="0.06">
207
- <name>AB</name>
208
- <clade id_source="a" branch_length="0.102">
209
- <name>A</name>
210
- </clade>
211
- <clade id_source="b" branch_length="0.23">
212
- <name>B</name>
213
- </clade>
214
- </clade>
215
- <clade id_source="c" branch_length="0.4">
216
- <name>C</name>
217
- </clade>
218
- </clade>
219
- <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>
220
- </phylogeny>
221
- <phylogeny rooted="true">
222
- <name>same example, using property elements to indicate a "depth" value for marine organisms</name>
223
- <clade>
224
- <clade>
225
- <name>AB</name>
226
- <clade>
227
- <name>A</name>
228
- <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 1200 </property>
229
- </clade>
230
- <clade>
231
- <name>B</name>
232
- <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 2300 </property>
233
- </clade>
234
- </clade>
235
- <clade>
236
- <name>C</name>
237
- <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
238
- </clade>
239
- </clade>
240
- </phylogeny>
241
- <phylogeny rooted="true">
242
- <name>same example, using property elements to indicate a "depth" value for marine organisms by using id refs in
243
- order to have property elements outside of the tree topology</name>
244
- <clade>
245
- <clade>
246
- <name>AB</name>
247
- <clade id_source="id_a">
248
- <name>A</name>
249
- </clade>
250
- <clade id_source="id_b">
251
- <name>B</name>
252
- </clade>
253
- </clade>
254
- <clade id_source="id_c">
255
- <name>C</name>
256
- </clade>
257
- </clade>
258
- <property id_ref="id_a" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 1200 </property>
259
- <property id_ref="id_b" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 2300 </property>
260
- <property id_ref="id_c" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 200 </property>
261
- </phylogeny>
262
- <phylogeny rooted="true">
263
- <name>monitor lizards</name>
264
- <description>a pylogeny of some monitor lizards</description>
265
- <clade>
266
- <taxonomy>
267
- <id provider="NCBI">8556</id>
268
- <scientific_name>Varanus</scientific_name>
269
- <rank>genus</rank>
270
- <uri desc="EMBL REPTILE DATABASE">http://www.embl-heidelberg.de/~uetz/families/Varanidae.html</uri>
271
- </taxonomy>
272
- <clade>
273
- <taxonomy>
274
- <id provider="NCBI">62046</id>
275
- <scientific_name>Varanus niloticus</scientific_name>
276
- <common_name>Nile monitor</common_name>
277
- <rank>species</rank>
278
- </taxonomy>
279
- <distribution>
280
- <desc>Africa</desc>
281
- </distribution>
282
- </clade>
283
- <clade>
284
- <taxonomy>
285
- <scientific_name>Odatria</scientific_name>
286
- <rank>subgenus</rank>
287
- </taxonomy>
288
- <clade>
289
- <taxonomy>
290
- <id provider="NCBI">169855</id>
291
- <scientific_name>Varanus storri</scientific_name>
292
- <common_name>Storr's monitor</common_name>
293
- <rank>species</rank>
294
- </taxonomy>
295
- <distribution>
296
- <desc>Australia</desc>
297
- </distribution>
298
- </clade>
299
- <clade>
300
- <taxonomy>
301
- <id provider="NCBI">62053</id>
302
- <scientific_name>Varanus timorensis</scientific_name>
303
- <common_name>Timor monitor</common_name>
304
- <rank>species</rank>
305
- </taxonomy>
306
- <distribution>
307
- <desc>Asia</desc>
308
- </distribution>
309
- </clade>
310
- </clade>
311
- </clade>
312
- </phylogeny>
313
- <phylogeny rooted="true">
314
- <name>A tree with phylogeographic information</name>
315
- <clade>
316
- <clade>
317
- <clade>
318
- <name>A</name>
319
- <distribution>
320
- <desc>Hirschweg, Winterthur, Switzerland</desc>
321
- <point geodetic_datum="WGS84">
322
- <lat>47.481277</lat>
323
- <long>8.769303</long>
324
- <alt>472</alt>
325
- </point>
326
- </distribution>
327
- </clade>
328
- <clade>
329
- <name>B</name>
330
- <distribution>
331
- <desc>Nagoya, Aichi, Japan</desc>
332
- <point geodetic_datum="WGS84">
333
- <lat>35.155904</lat>
334
- <long>136.915863</long>
335
- <alt>10</alt>
336
- </point>
337
- </distribution>
338
- </clade>
339
- <clade>
340
- <name>C</name>
341
- <distribution>
342
- <desc>ETH Zürich</desc>
343
- <point geodetic_datum="WGS84">
344
- <lat>47.376334</lat>
345
- <long>8.548108</long>
346
- <alt>452</alt>
347
- </point>
348
- </distribution>
349
- </clade>
350
- </clade>
351
- <clade>
352
- <name>D</name>
353
- <distribution>
354
- <desc>San Diego</desc>
355
- <point geodetic_datum="WGS84">
356
- <lat>32.880933</lat>
357
- <long>-117.217543</long>
358
- <alt>104</alt>
359
- </point>
360
- </distribution>
361
- </clade>
362
- </clade>
363
- </phylogeny>
364
- <phylogeny rooted="true">
365
- <name>A tree with date information</name>
366
- <clade>
367
- <clade>
368
- <clade>
369
- <name>A</name>
370
- <date unit="mya">
371
- <desc>Silurian</desc>
372
- <value>425</value>
373
- </date>
374
- </clade>
375
- <clade>
376
- <name>B</name>
377
- <date unit="mya">
378
- <desc>Devonian</desc>
379
- <value>320</value>
380
- </date>
381
- </clade>
382
- </clade>
383
- <clade>
384
- <name>C</name>
385
- <date unit="mya">
386
- <desc>Ediacaran</desc>
387
- <value>600</value>
388
- <minimum>570</minimum>
389
- <maximum>630</maximum>
390
- </date>
391
- </clade>
392
- </clade>
393
- </phylogeny>
394
- <phylogeny rooted="true">
395
- <name>Using another XML language to store an alignment</name>
396
- <clade>
397
- <clade>
398
- <clade>
399
- <name>A</name>
400
- </clade>
401
- <clade>
402
- <name>B</name>
403
- </clade>
404
- </clade>
405
- <clade>
406
- <name>C</name>
407
- </clade>
408
- </clade>
409
- </phylogeny>
410
- <align:alignment xmlns:align="http://example.org/align">
411
- <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>
412
- <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>
413
- <seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq>
414
- </align:alignment>
415
- </phyloxml>