PhyloXML

PhyloXML is an XML-based data exchange format for phylogenetic trees with richly annotated metadata. The format provides a standardized schema to encode tree topology together with data about taxa, evolutionary events, branch lengths, support values, sequences, publications, and provenance. A PhyloXML document centers on one or more phylogeny elements that contain nested clades, each of which can carry a name and optional attributes such as branch lengths and confidence values; additional sections describe taxa and their taxonomy, associated sequences, and metadata about publications or references. Files can be validated against an XML schema (XSD), enabling reliable data exchange between software tools. PhyloXML is extensible, allowing researchers to attach custom annotations through a standard mechanism while preserving compatibility with existing data. It complements simpler formats such as Newick by enabling rich annotations at the tree and taxon level, and is used in a variety of phylogenetics workflows and publications. Common considerations include verbosity and file size, and the need for tools that can export or import PhyloXML. The format is commonly stored with the .phyloxml extension and is supported by multiple software ecosystems for phylogenetic analysis and visualization.