PhyloXML is an

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. T ...

language for the analysis, exchange, and storage of

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

s (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (

XSD XSD (XML Schema Definition), a recommendation of the World Wide Web Consortium ( W3C), specifies how to formally describe the elements in an Extensible Markup Language (XML) document. It can be used by programmers to verify each piece of item con ...

) language. A shortcoming of current formats for describing phylogenetic trees (such as

Nexus NEXUS is a joint Canada Border Services Agency and U.S. Customs and Border Protection-operated Trusted Traveler and Border control#Expedited border controls, expedited border control program designed for pre-approved, low-risk travelers. Members ...

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 ''Archaeopteryx'' (; ), sometimes referred to by its German name, "" ( ''Primeval Bird''), is a genus of bird-like dinosaurs. The name derives from the ancient Greek (''archaīos''), meaning "ancient", and (''ptéryx''), meaning "feather" ...

Basic phyloXML example

example from Prof. Joe Felsenstein's book "Inferring Phylogenies" MrBayes based on MAFFT alignment 0.88 A B C

References

External links

www.phyloxml.orgArchaeopteryx program
{{genomics-footer XML-based standards Phylogenetics software Biological_sequence_format