PhyloXML is a historical xml format created in 2009. PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language. A shortcoming of current formats for describing phylogenetic trees (such as Nexus and Newick/New Hampshire) is a lack of a standardized means to annotate tree nodes and branches with distinct data fields (which in the case of a basic species tree might be: species names, branch lengths, and possibly multiple support values). Read more on Wikipedia...

10Years Old 25Users 0Jobs

Example code from the web:

 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"
  xmlns="http://www.phyloxml.org">
  <phylogeny rooted="true">
     <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
     <description>MrBayes based on MAFFT alignment</description>
     <clade>
        <clade branch_length="0.06">
           <confidence type="probability">0.88</confidence>
           <clade branch_length="0.102">
              <name>A</name>
           </clade>
           <clade branch_length="0.23">
              <name>B</name>
           </clade>
        </clade>
        <clade branch_length="0.4">
           <name>C</name>
        </clade>
     </clade>
  </phylogeny>
</phyloxml>

Example code from Wikipedia:

<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"
   xmlns="http://www.phyloxml.org">
   <phylogeny rooted="true">
      <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
      <description>MrBayes based on MAFFT alignment</description>
      <clade>
         <clade branch_length="0.06">
            <confidence type="probability">0.88</confidence>
            <clade branch_length="0.102">
               <name>A</name>
            </clade>
            <clade branch_length="0.23">
               <name>B</name>
            </clade>
         </clade>
         <clade branch_length="0.4">
            <name>C</name>
         </clade>
      </clade>
   </phylogeny>
 </phyloxml>

Last updated October 14th, 2019