May 26, 2018
Software toolkit for phylogenetic inference
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.