A Julia implementation of the method described in:
Pagel, Mark. "Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters." Proceedings of the Royal Society of London. Series B: Biological Sciences 255.1342 (1994): 37-45.
With some extensions that, in principle, allow you to model arbitrary numbers of characters and states.
This is a research prototype; you would be a fool to attempt to use it.
You'll need a recent version of Julia (>=0.2.0).
Pkg.clone("https://github.com/porterjamesj/Pagel.jl.git")
using Pagel
The module exports a single function, maxlikelihood, whoose interface is:
maxlikelihood(model,treefile,statesfile)
Where model is one of :dependant or :independant, and treefile and statefile
are your data. treefile should just have a single newick string in it (not a NEXUS
file), states should be pretty much exactly what you would use for BayesTraits.