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Bioinformatics Advance Access originally published online on February 24, 2006
Bioinformatics 2006 22(8):1004-1006; 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

Paloverde: an OpenGL 3D phylogeny browser

Michael J. Sanderson

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

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 3D world in which a large tree presented in various layouts can be manipulated through a mouse interface. The program implements radial 2D layouts, and true 3D 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 3D 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 dataset.

Contact: mjsanderson{at}ucdavis.edu

Received on December 11, 2005; revised on January 26, 2006; accepted on February 3, 2006

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[Abstract] [Full Text] [PDF]


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