PhyloXML

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