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Start Your TrialPhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. The main distinguishing feature of PhyloBayes is its use of the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments, as it allows selection to be evaluated separately for each position in a sequence..
PhlyoBayes MPI on XSEDE provides a primitive interface that submits jobs to Expanse, a large NSF XSEDE Resource. Please let us know if you have trouble using the interface.
PhyloBayes MPI supports checkpointing, which makes it possible to restart a run that has terminated unexpectedly, or that has reached the end of the maximum allowed run time without converging.
However,
Manual for PhyloBayes MPI 1.9 (pdf)
PhyloBayes MPI home page here.
INPUT = dna or protein matrices in relaxed Phylip format
OUTPUT = A set of files the most important of which are:
If you use PhyloBayesMPI, please cite: Nicolas Lartillot, Nicolas Rodrigue, Daniel Stubbs, Jacques Richer, PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment, Systematic Biology, Volume 62, Issue 4, July 2013, Pages 611–615, doi.org/10.1093/sysbio/syt022
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