PhyloXML

PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data.[1] The structure of phyloXML is described by XML Schema Definition (XSD) language.

PhyloXML
Filename extensions.phyloxml
Internet media typetext/x-phyloxml+xml
Developed byMira V Han and Christian M Zmasek
Initial release27 October 2009 (2009-10-27)
Type of formatphylogenetic trees
Extended fromXML
Open format?Yes
Websitephyloxml.org

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.

Basic phyloXML example

 
<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" 
  xmlns="http://www.phyloxml.org">
  <phylogeny rooted="true">
    <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
    <description>MrBayes based on MAFFT alignment</description>
    <clade>
      <clade branch_length="0.06">
        <confidence type="probability">0.88</confidence>
        <clade branch_length="0.102">
          <name>A</name>
        </clade>
        <clade branch_length="0.23">
          <name>B</name>
        </clade>
      </clade>
      <clade branch_length="0.5">
        <name>C</name>
      </clade>
    </clade>
  </phylogeny>
</phyloxml>
gollark: As I said to sinþ:> If you actually are interested, the basic idea is just Notes Application #129719257 designed vaguely around wiki principles and as a shiny JS-based SPA.
gollark: I have a list of extra necessary stuff:```* Tags* Revision history* Media handling* Metadata/structured data support? At least for media* Usable mobile support* Search!* Efficient space use - compression?* Make inter-device synchronization possible* Consistent scrolling behavior* Probably some kind of macro-y or extension feature for important stuff like embedding maths/PDFs```which I expect to never finish.
gollark: So far I have:- page viewing capability (Markdown → virtual-DOM HTML)- page editing/creating capability (literally a `textarea`)but that's... basically it?
gollark: Anyway, if anyone wants to contribute code that would be appreciated. I'm not releasing the current code because I do not like it and it is unfinished, so just guess what code I might want and send me it.
gollark: The sanity thing, I mean.

References
  1. Han, Mira V.; Zmasek, Christian M. (2009). "phyloXML: XML for evolutionary biology and comparative genomics". BMC Bioinformatics. United Kingdom: BioMed Central. 10: 356. doi:10.1186/1471-2105-10-356. PMC 2774328. PMID 19860910.
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