<?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>
