Paloverde: an OpenGL 3D phylogeny browser.

UNLABELLED: 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.