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Bioinformatics Advance Access published online on February 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl044
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 11, 2005
Revised January 26, 2006
Accepted February 3, 2006

Applications note

Paloverde: an OpenGL 3-D phylogeny browser

Michael J. Sanderson 1 *

1 Section of Evolution and Ecology, University of California, Davis, CA, USA

* To whom correspondence should be addressed.
Michael J. Sanderson, E-mail: mjsanderson{at}ucdavis.edu


  Abstract

Summary: Paloverde is a new program designed to help visualize the phylogenetic structure of moderately large trees--trees on the scale of 100-2500 leaf nodes. The program embeds the user in an interactive virtual 3-D world in which a large tree presented in various layouts can be manipulated through a mouse interface. The program implements radial 2-D layouts, and true 3-D spiral, conical, and hemispherical (i.e., truly "tree"-like) layouts. Subclades can be defined in the input file (using standard node-based definitions) and displayed collapsed as new leaf nodes, or left intact but annotated with names around the periphery of the tree. A search tool lets the user zoom to any selected leaf node. Paloverde is an open source project written in ANSI C using the OpenGL library for 3-D visualization.

Availability: Source code, makefiles for Mac OS X and Linux, and a compiled binary for Mac OS X are available at http://ginger.ucdavis.edu/paloverde/paloverde.html, along with a sample data set.

Associate Editor: Keith A Crandall
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