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<?xml version="1.0" encoding="UTF-8"?>
<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">
<phylogeny rooted="true" rerootable="false" branch_length_unit="1">
<name>testing confidence</name>
<confidence type="bootstrap">89</confidence>
<confidence type="probability">0.71</confidence>
<clade>
<name>b</name>
<width>0.2</width>
<clade>
<name>c</name>
<color>
<red>128</red>
<green>220</green>
<blue>28</blue>
</color>
<confidence type="probability">0.9</confidence>
<confidence type="probability">0.71</confidence>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>testing polygon</name>
<clade>
<clade>
<name>A</name>
<distribution>
<desc>Polygon from random points</desc>
<polygon>
<point geodetic_datum="WGS84" alt_unit="m">
<lat>47.481277</lat>
<long>8.769303</long>
<alt>472</alt>
</point>
<point geodetic_datum="WGS84">
<lat>35.155904</lat>
<long>136.915863</long>
<alt>10</alt>
</point>
<point geodetic_datum="WGS84">
<lat>47.376334</lat>
<long>8.548108</long>
<alt>452</alt>
</point>
</polygon>
<polygon>
<point geodetic_datum="WGS84">
<lat>40.481277</lat>
<long>8.769303</long>
<alt>42</alt>
</point>
<point geodetic_datum="WGS84">
<lat>25.155904</lat>
<long>136.915863</long>
<alt>10</alt>
</point>
<point geodetic_datum="WGS84">
<lat>47.376334</lat>
<long>7.548108</long>
<alt>452</alt>
</point>
</polygon>
</distribution>
</clade>
<clade>
<name>B</name>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>testing references</name>
<clade>
<clade>
<name>A</name>
<reference doi="10.1093/bioinformatics/btm619">
<desc>Phyutility: a phyloinformatics tool for trees, alignments and molecular data</desc>
</reference>
<reference doi="10.1186/1471-2105-9-S1-S23"></reference>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<clade>
<name>A</name>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>Example of domain. Taken from apaf.mxl</name>
<clade>
<clade>
<name>22_MOUSE</name>
<branch_length>0.05998</branch_length>
<taxonomy>
<code>MOUSE</code>
<synonym>murine</synonym>
<synonym>vermin</synonym>
</taxonomy>
<sequence>
<annotation>
<desc>alcohol dehydrogenase</desc>
<confidence type="probability">0.99</confidence>
<property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m">1200</property>
</annotation>
<domain_architecture length="1249">
<domain from="6" to="90" confidence="7.0E-26" id="x">CARD</domain>
<domain from="109" to="414" confidence="7.2E-117">NB-ARC</domain>
<domain from="605" to="643" confidence="2.4E-6">WD40</domain>
<domain from="647" to="685" confidence="1.1E-12">WD40</domain>
<domain from="689" to="729" confidence="2.4E-7">WD40</domain>
<domain from="733" to="771" confidence="4.7E-14">WD40</domain>
<domain from="872" to="910" confidence="2.5E-8">WD40</domain>
<domain from="993" to="1031" confidence="4.6E-6">WD40</domain>
<domain from="1075" to="1113" confidence="6.3E-7">WD40</domain>
<domain from="1117" to="1155" confidence="1.4E-7">WD40</domain>
<domain from="1168" to="1204" confidence="0.3">WD40</domain>
</domain_architecture>
</sequence>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true" rerootable="false">
<name>dollo_on_domains__cofilin_e1/o_tol_332</name>
<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>
<confidence type="parsimony">4.0</confidence>
<clade>
<name>cellular_organisms</name>
<binary_characters type="parsimony inferred" gained_count="0" lost_count="0" present_count="0">
</binary_characters>
<clade>
<name>Neomura</name>
<binary_characters type="parsimony inferred" gained_count="0" lost_count="0" present_count="0">
</binary_characters>
<clade>
<name>Eukaryota</name>
<binary_characters type="parsimony inferred" gained_count="2" lost_count="0" present_count="2">
<gained>
<bc>Cofilin_ADF</bc>
<bc>Gelsolin</bc>
</gained>
<present>
<bc>Cofilin_ADF</bc>
<bc>Gelsolin</bc>
</present>
</binary_characters>
</clade>
</clade>
</clade>
</phylogeny>
</phyloxml>
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