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Bioinformatics Advance Access originally published online on February 4, 2009
Bioinformatics 2009 25(5):672-673; doi:10.1093/bioinformatics/btp044
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Jacqueline Whalley 1, Stephen Brooks 2 and Robert G. Beiko 2,*

1School of Computing and Mathematical Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand and 2Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, Canada B3H 1W5

*To whom correspondence should be addressed.


  Abstract

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{at}cs.dal.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on November 16, 2008; revised on January 16, 2009; accepted on January 16, 2009

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