phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to extensible nature of XML itself and the provision of <property> elements by phyloXML, extensibility as well as domain specific applications are ensured. The structure of phyloXML is described by XML Schema Definition (XSD) language.
1. Download the newest version of the forester libraries:
2. Download an example phyloXML file:
» apaf.xml (Apaf-1 gene family tree with domain architectures) or
» bcl_2.xml (Bcl-2 gene family tree with gene duplications, support values, and taxonomy data)
3. Click on file "forester.jar" (Archaeopteryx should start; or use "java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx") and use "File"|"Read tree from file..." to load file "bcl_2.xml" or "apaf.xml".
Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types.
A well defined XML format addresses these problems in a general and extensible manner and allows for interoperability, both between and in between specialized and general purpose software.
Christian Zmasek | phyloxml -at- gmail -dot- com
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Archaeopteryx | forester