Paloverde v. 1.1
A 3-D tree visualization tool
M.J. Sanderson, January 2006
Section of Evolution and Ecology
UC Davis
Davis, CA 95616 USA




INTRODUCTION

This is a simple program to do three-D visualizations of moderately large phylogenies. Trees with between 100 and 2500 taxa seem to work best (more if subclades are defined by the user). Faster graphics hardware than is available by default on my Powerbook G4 laptop extend the range upward, as does a large "cinema" display.

The program allows the user to examine the tree from various perspectives and distances. The basic "circle" layout has the most features, but three true 3-D layouts are also available (spiral, cone, and hemispheric, or truly "tree-like"). Several display modes are provided that change the kind of information displayed on large trees, especially with respect to user-defined subclades. These can be defined by the user in the input file, or they can be generated on the fly based on grouping, e.g., all species in the same (monophyletic) "genus" together. Subclades can be displayed as single terminal taxa or they can be displayed in their entirety with visual cues about their membership. A pop-up menu permits the user to select any of these subclades, which are then presented in their own 3D world. Finally, a search tool lets the user zoom to any terminal taxon.

For users of Mac OS 10.3 and later, a binary executable can be downloaded below. You can also download the source code and compile it on Linux quite easily. The makefiles can be modified to compile on other systems. The program is written in C using the OpenGL graphics library and two libraries for phylogenetics programs that I have written, also in C (available in the source distribution). This is my first openGL program, and it undoubtedly does a lot of things inefficiently or inelegantly. I welcome suggestions for improvement (mjsanderson@ucdavis.edu).

INSTALLATION (executable for Mac OS 10.3)

        Download the README file, the sample data file, and the executable file from the web site and follow the installation instructions in the README.

INSTALLATION (Compiling from source code for Linux or other systems)
        Download the distribution and source code (tar.Z file), uncompress and untar the archive and follow the installation instructions in the README.

BUG FIXES AND FEATURE CHANGES

12.20.2005 -- Subtrees drawn with the popup window feature were not always displaying all taxa (fixed).
1.25.2005 -- Several bugs fixed with label displays; addition of search tool.