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:
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>