phyloXML
XML for evolutionary biology and comparative genomics

Summary

phyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language.

News

2009.07.03: Beta version for phyloXML 1.10 released: http://www.phyloxml.org/1.10/phyloxml.xsd

2009.06.26: Proposed changes for version 1.10: phyloxml.blogspot.com

2009.04.20: BioPython (»project page, »wiki, »source code) and BioRuby (»project page, »wiki, »source code) implementations of the phyloXML format are being supported by Google Inc. as part of the Google Summer of Code™ 2009 program and sponsored by the National Evolutionary Synthesis Center (NESCent) as part of the Phyloinformatics Summer of Code 2009.

Documentation

• detailed
• overview [png]

XML Schema Definition Location

http://www.phyloxml.org/1.00/phyloxml.xsd

Try it!

Online (Archaeopteryx):

• Apaf-1 (domain architectures)
• Bcl-2 (gene duplications, support values, and taxonomy data)
• Amphibian species tree
• Mollusk taxonomy (Mollusca from the NCBI taxonomy with 5632 external nodes)

Locally:

1. Download the newest version of the forester libraries: » forester.jar
2. Download an example phyloXML file:
» bcl_2.xml (Bcl-2 gene family tree with gene duplications, support values, and taxonomy data) or
» apaf.xml (Apaf-1 gene family tree with domain architectures) or
» ncbi_taxonomy_mollusca.xml.zip (Mollusca from the NCBI taxonomy with 5632 external nodes)
3. Click on file "forester.jar" (ATV should start; or use "java -cp path\to\forester.jar org.forester.atv.ATV") and use "File"|"Read tree from file..." to load file "bcl_2.xml", "apaf.xml", or "ncbi_taxonomy_mollusca.xml.zip".

Rationale

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: taxon 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, both between and in between specialized and general purpose software.

Feature Highlights

• Basic species trees can be described with clade, name, distance, and possibly confidence elements
• Examples of some elements for more specialized analyzes: taxonomic information with scientific name, common name, and taxonomy code; sequence data with gene name, sequence accession, and annotation; distribution; branch lengths and support values; events such as duplications and speciations; control of tree appearance with colors and branch widths
• Property elements allow the addition of domain specific textual and numerical data
• Capability to describe relations between nodes (e.g. to describe nodes with more than one parent), and between sequences (e.g. to express orthology relationships).

Examples

• phyloxml_examples.xml
• » ncbi_taxonomy_metazoa.xml.zip (Metazoa from the NCBI taxonomy with 73907 external nodes)
• » tol_life_on_earth_1.xml.zip (complete 'life on earth' phylogeny from the Tree of Life project with 57124 external nodes)

Resources

• Display: Archaeopteryx
• BioPerl implementation
• Phyloxml converter (newick to phyloxml): phyloxml_converter
• Phylogeny decorator: decorator
• Example of a basic XSLT to transform phyloXML node names to HTML: » phyloxml_to_html_xslt.xml
• BioRuby implementation (in progress) (»wiki, »source code, »project plan)
• BioPython implementation (in progress) (»wiki, »source code, »project plan)

phyloXML Support and Applications (examples)

BioPerl (project demo) | TreeViewJ | TreeGradients | Archaeopteryx | phyloxml_converter | decorator

Bookmark This

Delicious | | Hatena Bookmark

Yahoo phyloXML Group

The purposes of this group are (i) to inform about new developments concerning phyloXML and (ii) to provide a platform for discussing ideas regarding phyloXML.

groups.yahoo.com/group/phyloxml

Other Relevant XML Efforts

Retree | TreeML | NeXML | GraphML | Representation and Retrieval Method for Molecular Phylogenetic Tree Data Based on XML [Joho Shori Gakkai Kenkyu Hokoku article] | Taxonomic markup language [Bioinformatics article] | XGMML (eXtensible Graph Markup and Modeling Language) | BioPax | GraphXML [pdf] | XML for Molecular Biology as compiled by Paul Gordon | XML-biology links

Acknowledgements

Many of the ideas for the phyloXML format are the results of discussions by the members of the phyloXML discussion group. Ethalinda Cannon contributed to the development of ATV/Archaeopteryx and phyloXML. Additional progress on phyloXML and its implementations are due to the BioHackathon 2008 (towards integrated web service in life science with Open Bio* libraries). The BioPerl implementation of the phyloXML format was supported by Google Inc. as part of the Google Summer of Code™ 2008 program and was sponsored by the National Evolutionary Synthesis Center (NESCent).

Contacts

Christian M Zmasek | Burnham Institute for Medical Research | cmzmasek yahoo com

Last updated: 2009.07.03

phyloXML blog | Archaeopteryx | forester | www.phylosoft.org