PhyloXML

XML language for the analysis, exchange, and storage of phylogenetic trees

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Added 9 Jul 2026

Edited 9 Jul 2026 · history

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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.

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)

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www.phyloxml.org

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PhyloXML

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