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Bioinformatics Advance Access published online on February 8, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn038
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Interactive Visualization Software for Exploring Phylogenetic Trees and Clades

Mark Derthick

Human-Computer Interaction Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA, mad@cs.cmu.edu

To whom correspondence should be addressed. Mr. Mark Derthick, E-mail: mad{at}cs.cmu.edu


  Abstract

The Summary Tree Explorer (STE) is a Java application for interac-tively exploring sets of phylogenetic trees using two coupled repre-sentations: a node-and-link diagram and a textual list of common clades. Selection, pruning, filtering, or re-rooting in one representa-tion is immediately reflected in the other. While summary trees are more effective at showing the relationship among clades, they can only show a consistent subset of those that appear in the textual list. Working with both representations mitigates the disadvantages of having to choose just one.

STE, along with several sample datasets, is available at http://cityscape.inf.cs.cmu.edu/phylogeny/

Associate Editor: Prof. Martin Bishop

Received on November 8, 2007; revised on January 23, 2008; accepted on January 24, 2008

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