Introduction

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.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.

Publications

  1. Paloverde: an OpenGL 3D phylogeny browser.
    Cite this
    Sanderson MJ, 2006-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Michael J Sanderson
    Investigator

    Section of Evolution and Ecology, University of California

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Summary
AccessionBT000391
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByMichael J Sanderson