Pagel.jl

Detect correlated evolution on phylogenies
Popularity
2 Stars
Updated Last
7 Years Ago
Started In
November 2013

Pagel.jl

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.

WARNING

This is a research prototype; you would be a fool to attempt to use it.

Use

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.