bio-phyloxml 0.9.0
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- data/.document +5 -0
- data/.travis.yml +12 -0
- data/Gemfile +13 -0
- data/LICENSE.txt +20 -0
- data/README.md +199 -0
- data/README.rdoc +48 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/lib/bio-phyloxml.rb +12 -0
- data/lib/bio/phyloxml.rb +3 -0
- data/lib/bio/phyloxml/elements.rb +1166 -0
- data/lib/bio/phyloxml/parser.rb +1000 -0
- data/lib/bio/phyloxml/phyloxml.xsd +582 -0
- data/lib/bio/phyloxml/writer.rb +227 -0
- data/sample/test_phyloxml_big.rb +205 -0
- data/test/data/phyloxml/apaf.xml +666 -0
- data/test/data/phyloxml/bcl_2.xml +2097 -0
- data/test/data/phyloxml/made_up.xml +144 -0
- data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
- data/test/data/phyloxml/phyloxml_examples.xml +415 -0
- data/test/helper.rb +25 -0
- data/test/unit/bio/test_phyloxml.rb +821 -0
- data/test/unit/bio/test_phyloxml_writer.rb +334 -0
- metadata +155 -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>
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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>
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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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82
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+
<sequence>
|
|
83
|
+
<annotation>
|
|
84
|
+
<desc>alcohol dehydrogenase</desc>
|
|
85
|
+
<confidence type="probability">0.91</confidence>
|
|
86
|
+
</annotation>
|
|
87
|
+
</sequence>
|
|
88
|
+
</clade>
|
|
89
|
+
</clade>
|
|
90
|
+
<clade>
|
|
91
|
+
<name>C</name>
|
|
92
|
+
<taxonomy>
|
|
93
|
+
<scientific_name>C. elegans</scientific_name>
|
|
94
|
+
</taxonomy>
|
|
95
|
+
<sequence>
|
|
96
|
+
<annotation>
|
|
97
|
+
<desc>alcohol dehydrogenase</desc>
|
|
98
|
+
<confidence type="probability">0.67</confidence>
|
|
99
|
+
</annotation>
|
|
100
|
+
</sequence>
|
|
101
|
+
</clade>
|
|
102
|
+
</clade>
|
|
103
|
+
</phylogeny>
|
|
104
|
+
<phylogeny rooted="true">
|
|
105
|
+
<name>same example, with gene duplication information and sequence relationships</name>
|
|
106
|
+
<clade>
|
|
107
|
+
<events>
|
|
108
|
+
<speciations>1</speciations>
|
|
109
|
+
</events>
|
|
110
|
+
<clade>
|
|
111
|
+
<events>
|
|
112
|
+
<duplications>1</duplications>
|
|
113
|
+
</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>
|