TY - JOUR
T1 - RevBayes
T2 - Bayesian phylogenetic inference using graphical models and an interactive model-specification language
AU - Hohna, Sebastian
AU - Landis, Michael J.
AU - Heath, Tracy A.
AU - Boussau, Bastien
AU - Lartillot, Nicolas
AU - Moore, Brian R.
AU - Huelsenbeck, John P.
AU - Ronquist, Fredrik
N1 - Funding Information:
This work was supported by the Miller Institute for basic research in science [to S.H.]; National Science of Foundation (NSF) [grant DEB-1256993 to T.A.H.]; NSF [grants DEB-DEB-0842181, DEB-0919529, DBI-1356737, and DEB-1457835 to B.R.M.]; and the Swedish Research Council [grant 2011-5622 to F.R.].
Publisher Copyright:
© The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
PY - 2016/7
Y1 - 2016/7
N2 - Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogeneticgraphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complexmodels. Fortunately, this tremendous flexibility does not come at the cost of slower computation; aswe demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com.
AB - Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogeneticgraphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complexmodels. Fortunately, this tremendous flexibility does not come at the cost of slower computation; aswe demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com.
KW - Bayesian inference
KW - Graphical models
KW - MCMC
KW - Statistical phylogenetics
UR - http://www.scopus.com/inward/record.url?scp=84979285130&partnerID=8YFLogxK
U2 - 10.1093/sysbio/syw021
DO - 10.1093/sysbio/syw021
M3 - Article
C2 - 27235697
AN - SCOPUS:84979285130
SN - 1063-5157
VL - 65
SP - 726
EP - 736
JO - Systematic Biology
JF - Systematic Biology
IS - 4
ER -