Journal Article

Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree

Jacqueline Whalley, Stephen Brooks and Robert G. Beiko

in Bioinformatics

Volume 25, issue 5, pages 672-673
Published in print March 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp044
Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree

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Summary: A phenotypic character has a convex mapping to a given phylogenetic tree if each character state can be assigned a single point of origin in the tree. However, phenomena such as convergent evolution and lateral genetic transfer can lead to intermingling of character states and a consequent non-convex mapping. The phylogenetic heterogeneity of different characters can identify subsets of states that are non-randomly associated or which may have been transferred from one lineage to another. We have developed Radié, an interactive 3D Java application for mapping character states to the leaves and internal edges of a radial phylogenetic tree. In Radié each state of a given character is associated with a unique color, and internal edges with many descendant character states can be represented in a number of different ways to illustrate the diversity within each group.

Availability: Radié is freely available for download at http://kiwi.cs.dal.ca/~beiko/software-and-data/radie; source code is available upon request from the authors.

Contact: beiko@cs.dal.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1056 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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