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/