| PhyloXML | |
| Noextcode: | on |
| Nomimecode: | on |
| Mime: | text/x-phyloxml+xml |
| Developer: | Mira V Han and Christian M Zmasek |
| Genre: | phylogenetic trees |
| Extended From: | XML |
| Open: | Yes |
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.