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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/
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