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Crux is a software toolkit for molecular phylogenetic inference. It is
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structured as a set of Python modules, which makes it possible to quickly
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develop Python scripts that perform unique, non-canned analyses. Features
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include:
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* Tree log-likelihoods can be computed under a variety of models,
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including all specializations of GTR+I+G and mixture models. Tree
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likelihoods can be computed in parallel via pthreads.
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* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
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coupling) can sample among non-nested models using reversible model
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jumps.
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* Crux is capable of simulating character data under any model its
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likelihood engine is capable of.
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* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
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implementations are among the fastest in existence.
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* Pairwise distances between sequences can be computed based on percent
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identity, or using methods that correct for multiple hits
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(Jukes-Cantor, Kimura, and logDet).
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2009-06-09 01:49:59 +02:00
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WWW: http://www.canonware.com/Crux/
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