ArticleSystematic biology2016
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
Article in Systematic biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 292 papers, 1 of them a synthesis that pooled it.
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292 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.Systematic biology · 2024Pooled it
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- Sydney Phylogenetics Workshop: Lessons From the Past 15 Years.Ecology and evolution · 2026Article
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- A tale of two lineages: comparative biogeography across the Southern Cone of two South American Carex (Cyperaceae) groups.Annals of botany · 2026Article
- Review
- Inferring Branch-Specific Rates of Lineage Diversification Under the Birth-Death-Shift Process.Systematic biology · 2026Article
- Calibrating and documenting host-switching and evolution of incompatibility loci for two closely related Wolbachia clades.Genetics · 2026Article
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- Unidentifiability and false-positive inference in state-dependent diversification models.Nature communications · 2026Article
- Synnovation and confluence explain disparities in species richness across the Andes and Hengduan-Himalaya Mountains.Nature communications · 2026Article
- Bayesian credible sets for phylogenetic tree topologies with applications to coverage analysis and cross-model comparison.Molecular biology and evolution · 2026Article
- Evolution of fruit functional traits provides insights into the drivers of cycle-cup oaks (Plant diversity · 2026Article
- Niche evolution and asymmetric diversification in elm species (Ulmaceae).Plant diversity · 2026Article
- Physiology is a hidden dimension of diversity in the radiation of woodland salamanders.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- An Evolving View of Character Macroevolution.Systematic biology · 2026Review
- The Phylodynamic Threshold of Measurably Evolving Populations.Molecular biology and evolution · 2026Article
232 more citing papers are in PubMed but not listed here.
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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. Phylogenetic-graphical 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 complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we 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 [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.].
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.