PhyloXML
Encyclopedia
PhyloXML is an XML
language for the analysis, exchange, and storage of phylogenetic tree
s (or networks) and associated data. 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.
xmlns="http://www.phyloxml.org">
example from Prof. Joe Felsenstein's book "Inferring Phylogenies"
MrBayes based on MAFFT alignment
0.88
A
B
C
XML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
language for the analysis, exchange, and storage of phylogenetic tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
s (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language.
A shortcoming of current formats for describing phylogenetic trees (such as Nexus
Nexus file
Nexus file format is widely used in Bioinformatics. Several popular phylogenetic programs such as Paup*, MrBayes, Mesquite, and MacClade use this format.- Syntax :Command inside square brackets [ and ] are ignored...
and Newick/New Hampshire
Newick format
In mathematics, Newick tree format is a way to represent graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F...
) 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
xmlns="http://www.phyloxml.org">