Along with several colleagues, I am currently in the process of preparing a package, GEIGER, for the r
statistics package.
We have a beta version of GEIGER available:
CHANGES FROM LAST VERSION (0.2-4):
Fixed a bug that was preventing most functions from working on PC or unix machines.
by Luke J. Harmon, Jason Weir, Chad Brock, Richard E. Glor, and Wendell Challenger.
Install this using the "install from local source file" option in r.
I
think that the main useful functions of GEIGER will be:
1. Simulating phylogenies - simulate phylogenetic trees under
pure-birth and birth-death models; randomly prune any number of tips
from real or simulated trees.
2. Simulating character evolution - simulate character evolution for
n-dimensional continuous characters using multivariate Brownian motion;
simulate discrete characters with any given transition matrix.
3. Comparative analyses - convert between ape, pag (Pagel's continuous
and discrete programs), and OUCH (Butler and King's r package); carry
out loads of my own comparative tests, including disparity-through-time
from Harmon et al. 2003; maximum likelihood tests for discrete
character evolution.
Email me if you run into any snags.
Also
many of my papers mention that software is available for the
analyses; most of this is in c, and I'd be glad to send it to you, although we can now do almost everything in r.