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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

phyloXML: XML for evolutionary biology and comparative genomics.

Mira V Han¹, Christian M Zmasek

¹School of Informatics, Indiana University, Bloomington, IN 47408, USA. mirhan@indiana.edu

BMC Bioinformatics

|October 29, 2009

Summary

We developed phyloXML, an XML-based data standard for evolutionary trees, enabling comprehensive annotation of tree structures and associated data. This facilitates data exchange and analysis in biological studies.

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Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Evolutionary trees are fundamental in biological research, requiring annotation of nodes and branches with diverse data types.
Current data standards for evolutionary trees have limitations in accommodating various associated attributes.
Examples include taxonomic names, branch lengths, support values, gene data, and evolutionary events.

Purpose of the Study:

To introduce phyloXML, a novel XML language for describing evolutionary trees and their associated data.
To address the limitations of existing standards in handling diverse annotations.
To provide a flexible and extensible data format for evolutionary tree information.

Main Methods:

Development of phyloXML, an XML language with a defined schema (XSD).
Inclusion of specific elements for common tree annotations (e.g., branch lengths, support values, taxonomic names).
Utilization of flexible "property" elements for custom and unforeseen data types.

Main Results:

phyloXML enables the description of evolutionary tree structures and associated data items.
The format supports common annotations like branch lengths, support values, and taxonomic names.
phyloXML is adaptable to novel use cases through "property" elements.

Conclusions:

phyloXML is an XML language with a complete XSD schema for storing and exchanging evolutionary tree structures and associated data.
It offers a standardized solution for annotating evolutionary trees.
Tools for implementing and supporting phyloXML are available at http://www.phyloxml.org.