MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space - PubMed (original) (raw)

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space

Fredrik Ronquist et al. Syst Biol. 2012 May.

Abstract

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

PubMed Disclaimer

Similar articles

Cited by

References

    1. Altekar G, Dwarkadas S, Huelsenbeck J. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics. 2004;20:407–425. - PubMed
    1. Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst. Biol. 2012;61:170–173. - PMC - PubMed
    1. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4:e88. - PMC - PubMed
    1. Edwards SV, Liu L, Pearl DK. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 2007;104:5936–5941. - PMC - PubMed
    1. Gelman A, Rubin D. Inference from iterative simulation using multiple sequences. Stat. Sci. 1992;7:457–472.

Publication types

MeSH terms

Grants and funding

LinkOut - more resources