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Cited by 27,843

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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Ronquist, Fredrik, Teslenko, Maxim, van der Mark, Paul, Ayres, Daniel L., Darling, Aaron, Höhna, Sebastian, Larget, Bret, Liu, Liang, Suchard, Marc A., Huelsenbeck, John P.·2012·Systematic Biology
DOI 10.1093/sysbio/sys029
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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.

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Research works printed but not linked: 27

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Cited by

Metadata

Authors
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P.
Venue
Systematic Biology
Publisher
Oxford University Press (OUP)
Published
2012-02-22
Volume
61
Issue
3
Pages
539-542
ISSN
  • 1063-5157 (ISSN-L)
  • 1076-836X
DOI
10.1093/sysbio/sys029
OpenAlex
W2148698435
Cited by
27,843
References
6
FWCI
322.38
Type
journal article
Language
en
Open access
hybrid
Licence
creativecommons.org/licenses/by-nc/3.0 (vor, 1687 d)

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