BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

By Remco R. Bouckaert, Joseph Heled, Denise Kühnert, Timothy G. Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond. PLoS Comput. Biol., 2014

6,171 citations recorded by the source corpus.

We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1b8b81a1339c0a322e64acee9fc4a181188fcf9d

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Citations in the corpus

ASAP: assemble species by automatic partitioning (2020, methodology): “For GMYC and mGMYC, ultrametric trees were reconstructed using BEAST 2 (Bouckaert et al., 2014), with an independent GTR substitution model for each codon position.”
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, methodology): “is available as a package for BEAST 2 (Bouckaert et al. 2014).”
Bat Systematics in the Light of Unconstrained Analyses of a Comprehensive Molecular Supermatrix (2018, methodology): “We estimated the ages of nodes in the bat phylogeny using fossil calibration and a Bayesian framework with the BEAST 2 software v. 2.3.1 (Bouckaert et al. 2014).”
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 (2018, methodology): “2012), BEAST2 (Bouckaert et al. 2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al.”
Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. (2018, background): “1 mya) as well as the adaptive radiation of soritid foraminifera in the Eocene (55–42 mya; Figures S2A andS2B) in BEAST 2 [34] placed the age of the Symbiodiniaceae back to the middle Mesozoic at approximately 160 mya (posterior estimates; Figures 1A and 1B).”
Global gaps in trait data for terrestrial vertebrates (2020, methodology): “For plotting purposes, we obtained consensus trees using the TreeAnnotator program of the BEAST software (Bouckaert et al., 2014).”
Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera) (2018, background): “5 (Bouckaert et al., 2014) through the cipres science gate-”
Evolution of Oviposition Techniques in Stick and Leaf Insects (Phasmatodea) (2018, positive): “5) (Bouckaert et al., 2014) using 5 unambiguous crown-group phasmid fossils as minimum calibration points that we were able to assign to specific nodes on the tree using synapomorphy-based anatomical evidence (Bradler et al.”
Species Delimitation using Genome-Wide SNP Data (2013, methodology): “We analyzed these data using the modified version of SNAPP, which was implemented as a plug-in to the BEAST 2 (Bouckaert et al. 2014).”
Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot (2017, methodology): “For each clade, we assembled molecular sequence alignments (Dataset S1) and fossil calibration data and used relaxed molecular clock models implemented in BEAST (Bayesian Evolutionary Analysis Sampling Trees) (62, 63) to generate a Bayesian posterior sample of time-calibrated phylogenies and the ass”
High-level classification of the Fungi and a tool for evolutionary ecological analyses (2018, neutral): “(Bouckaert et al. 2014).”
Ancient hybridization fuels rapid cichlid fish adaptive radiations (2017, neutral): “71) and four different sets of calibration nodes (Supplementary Methods).”
bModelTest: Bayesian phylogenetic site model averaging and model comparison (2015, methodology): “For the α , we use the standard scale operator in BEAST 2 [13], adapted so it only samples if the category count flag is set for α .”