Crux is a software toolkit for molecular phylogenetic inference.  It is
structured as a set of Python modules, which makes it possible to quickly
develop Python scripts that perform unique, non-canned analyses.  Features
include:
* Tree log-likelihoods can be computed under a variety of models, including all
  specializations of GTR+I+G and mixture models.  Tree likelihoods can be
  computed in parallel via pthreads.
* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling)
  can sample among non-nested models using reversible model jumps.
* Crux is capable of simulating character data under any model its likelihood
  engine is capable of.
* The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations
  are among the fastest in existence.
* Pairwise distances between sequences can be computed based on percent
  identity, or using methods that correct for multiple hits (Jukes-Cantor,
  Kimura, and logDet).

WWW: http://www.canonware.com/Crux/
