{"doi":"10.1371/journal.pcbi.1003537","title":"BEAST 2: A Software Platform for Bayesian Evolutionary Analysis","abstract":"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.","journal":"PLoS Computational Biology","year":2014,"id":5056,"datarank":13.09077636209154,"base_score":8.842893331055539,"endowment":8.842893331055539,"self_citation_contribution":1.326433999658331,"citation_network_contribution":11.76434236243321,"self_endowment_contribution":1.326433999658331,"citer_contribution":11.76434236243321,"corpus_percentile":86.9,"corpus_rank":1865,"citation_count":6924,"citer_count":170,"citers_with_citation_signal":170,"citers_with_endowment":170,"datacite_reuse_total":0,"is_dataset":false,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2014-04-10","authors":[{"id":51518,"name":"Joseph Heled","orcid":"0000-0002-2403-7997","position":1,"is_corresponding":false},{"id":51519,"name":"Denise Kühnert","orcid":"0000-0002-5657-018X","position":2,"is_corresponding":false},{"id":51520,"name":"Tim Vaughan","orcid":null,"position":3,"is_corresponding":false},{"id":51521,"name":"Chieh-Hsi Wu","orcid":null,"position":4,"is_corresponding":false},{"id":44667,"name":"Dong Xie","orcid":"0000-0003-0878-3380","position":5,"is_corresponding":false},{"id":32104,"name":"Marc A. Suchard","orcid":"0000-0001-9818-479X","position":6,"is_corresponding":false},{"id":34991,"name":"Andrew Rambaut","orcid":"0000-0003-4337-3707","position":7,"is_corresponding":false},{"id":34990,"name":"Alexei J. Drummond","orcid":"0000-0003-4454-2576","position":8,"is_corresponding":false},{"id":51522,"name":"Chieh‐Hsi Wu","orcid":"0000-0001-9386-725X","position":9,"is_corresponding":false},{"id":51517,"name":"Remco Bouckaert","orcid":"0000-0001-6765-3813","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}