Table 1.

phyloXML elements and attributes summary

Element/Attribute	Description and Sub-elements
phylogeny	Represents a phylogeny, contains clades.
clade	Used recursively to represent node of a phylogeny.
taxonomy	Represents taxonomic information.
	id
	code
	scientific_name
	common_name
	synonym
	authority
sequence	A gene or protein associated with a clade.
	symbol
	accession
	name
	location
	mol_seq
	uri
	annotation
	domain_architecture
events	Events at a clade.
	type
	duplications
	speciations
	losses
	confidence
annotation	Annotation of sequence.
	desc
	confidence
	property
	uri
property	Typed and referenced mixed (free text) content.
uri	Uniform resource identifier (e.g. a URL).
confidence	Statistical confidence.
distribution	Geographic distribution of the items of a clade.
date	Date associated with a clade.
sequence_relation	Typed relationship between two sequences.
clade_relation	Typed relationship between two clades.
id_ref	Attribute, used together with id_source to describe relations between various elements.
id_source	Attribute, used together with id_ref to describe relations between various elements.

Representative elements and attributes of phyloXML (version 1.10) are shown. XML element/attribute names are in bold letters.