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.
