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.
| Filename extensions | .phyloxml |
|---|---|
| Internet media type | text/x-phyloxml+xml |
| Developed by | Mira V Han and Christian M Zmasek |
| Initial release | 27 October 2009 |
| Type of format | phylogenetic trees |
| Extended from | XML |
| Open format? | Yes |
| Website | phyloxml |
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.
Basic phyloXML example
<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>
References
- Han, Mira V.; Zmasek, Christian M. (2009). "phyloXML: XML for evolutionary biology and comparative genomics". BMC Bioinformatics. United Kingdom: BioMed Central. 10: 356. doi:10.1186/1471-2105-10-356. PMC 2774328. PMID 19860910.
