ICHEC Software

Crux

Versions Installed

Stokes: 1.1.0

Description

Crux is a software toolkit for molecular phylogenetic inference that runs on (at least) Linux, FreeBSD, and Mac OS X. It is structured as a set of Python modules, which makes it possible to quickly develop Python scripts that perform unique, non-canned analyses.

Crux's features include the following:

• Tree log-likelihoods can be computed under a variety of models, including all specializations of GTR+I+Γ and mixture models. Tree likelihoods can be computed in parallel via pthreads or MPI.
• Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling and MPI support for parallel computation) can sample among non-nested models using reversible model jumps. Polytomous trees can be sampled, also via reversible jumps. In fact, every non-essential model parameter that Crux's MCMC implementation estimates can be expunged via reversible jumps.
• Crux is capable of simulating character data under any model its likelihood engine is capable of. The huge range of simulation options makes a canned command line interface like that of Seq-Gen rather unwieldy, so simulation is perhaps the most obvious compelling reason to develop Crux scripts.
• The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations are among the fastest in existence, along with Clearcut.
• Pairwise distances between sequences can be computed based on percent identity, or using methods that correct for multiple hits (Jukes-Cantor, Kimura, and logDet).
• Multifurcating trees can be manipulated at a low level. Various standard operations are implemented, such as canonization (ordering the tree according to a ranking of the taxa), collapsing of zero-length branches, Robinson-Foulds distance computation, and so on.
• Parsers are included for various file formats, including Newick trees, FASTA sequences, and PHYLIP distance matrices.

License

Please refer to http://www.canonware.com/Crux/license.html for licensing information.

Benchmarks

N/A.

Additional Notes

To use Crux, load the relevant environment module "crux" along with other dependent modules:

Further information can be obtained from http://www.canonware.com/Crux/index.html