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/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>
84
- <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>
119
- <confidence type="parsimony">4.0</confidence>
120
- <clade>
121
- <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
@@ -1,415 +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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- <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>
96
- <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>
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- <clade>
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- <taxonomy>
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- <scientific_name>Bacillus subtilis</scientific_name>
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- </taxonomy>
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- <sequence id_source="x">
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- <symbol>adhB</symbol>
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- <accession source="ncbi">AAB80874</accession>
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- <name>alcohol dehydrogenase</name>
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- </sequence>
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- </clade>
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- <clade>
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- <taxonomy>
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- <scientific_name>Bacillus subtilis</scientific_name>
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- </taxonomy>
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- <sequence id_source="y">
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- <symbol>gbsB</symbol>
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- <accession source="ncbi">CAB15083</accession>
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- <name>alcohol dehydrogenase</name>
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- </sequence>
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- </clade>
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- </clade>
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- <clade>
136
- <taxonomy>
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- <scientific_name>Caenorhabditis elegans</scientific_name>
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- </taxonomy>
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- <sequence id_source="z">
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- <symbol>ADHX</symbol>
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- <accession source="ncbi">Q17335</accession>
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- <name>alcohol dehydrogenase</name>
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- <annotation ref="InterPro:IPR002085"/>
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- </sequence>
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- </clade>
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- </clade>
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- <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>
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- <sequence_relation id_ref_0="x" id_ref_1="z" type="orthology"/>
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- <sequence_relation id_ref_0="y" id_ref_1="z" type="orthology"/>
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- </phylogeny>
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- <phylogeny rooted="true">
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- <name>similar example, with more detailed sequence data</name>
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- <clade>
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- <clade>
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- <clade>
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- <taxonomy>
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- <id provider="NCBI">6645</id>
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- <code>OCTVU</code>
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- <scientific_name>Octopus vulgaris</scientific_name>
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- </taxonomy>
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- <sequence>
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- <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>