PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. ^[1] 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). Data storage and exchange is even more cumbersome in studies in which trees are the result of a reconciliation of some kind:

• gene-function studies (requires annotation of nodes with taxonomic information as well as gene names, and possibly gene-duplication data)
• evolution of host-parasite interactions (requires annotation of tree nodes with taxonomic information for both host and parasite)
• phylogeographic studies (requires annotation of tree nodes with taxonomic and geographic information)

To alleviate this, a variety of ad-hoc, special purpose formats have come into use (such as the NHX format, which focuses on the needs of gene-function and phylogenomic studies).

A well defined XML format addresses these problems in a general and extensible manner and allows for interoperability between specialized and general purpose software.

An example of a program for visualizing phyloXML is Archaeopteryx.

<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="0.5">
        <name>C</name>
      </clade>
    </clade>
  </phylogeny>
</phyloxml>

• www.phyloxml.org
• Archaeopteryx program