PhyloXML

PhyloXML is a 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...

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• PhyloXML ranks in the top 25% of languages
• the PhyloXML website
• the PhyloXML wikipedia page
• PhyloXML first appeared in 2009
• See also: xml, nexus-format, newick-format
• Have a question about PhyloXML not answered here? Email me and let me know how I can help.

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 February 18th, 2020

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