phyloXML

{{Short description|XML language variant}}

{{Infobox file format

| name = PhyloXML

| icon =

| iconcaption =

| screenshot =

| caption =

|_noextcode = on

| extensions = {{code|.phyloxml}}

|_nomimecode = on

| mime = text/x-phyloxml+xml

| type_code =

| uniform_type =

| conforms_to =

| magic =

| developer= Mira V Han and Christian M Zmasek

| released= {{start date and age|df=yes|paren=yes|2009|10|27}}

| latest_release_version =

| latest_release_date =

| genre = phylogenetic trees

| container_for =

| contained_by =

| extended_from = XML

| extended_to =

| standard =

| open = Yes

| url= {{URL|phyloxml.org}}

}}

PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data.{{cite journal | last = Han | first = Mira V. |author2=Zmasek, Christian M. | title = phyloXML: XML for evolutionary biology and comparative genomics | journal = BMC Bioinformatics | volume = 10| publisher = BioMed Central | location = United Kingdom | year = 2009 | pmid = 19860910 | pmc = 2774328 | doi = 10.1186/1471-2105-10-356 | pages = 356 | doi-access = free }} 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)
• 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.