The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The model implemented in BEAST2 allows transitions between conserved and accelerated rates in both directions.”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Bouckaert et al. 2014
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“As seen in figure 3, the accuracy of both methods increases as the ratio between accelerated and conserved rates increases”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Bouckaert et al. 2014
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
Self-citationTamura, K., & Nei, M. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040023 · Cited by 11,267
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss075 · Cited by 10,128
Self-citationDating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · cited 1×
“In particular it implements relaxed clocks [3], non-parametric coalescent analysis [4,5], multispecies coalescent inference [6], phylogeography [7,8] and others.”
MethodSelf-citationBayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
Drummond, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi103 · Cited by 3,094
Self-citation(1986) · Cited by 2,570
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
Self-citationBayesian Phylogeography Finds Its Roots
Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000520 · Cited by 1,784
Self-citationBeerli, P., & Felsenstein, J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081068098 · Cited by 1,701
Baele, G., Lemey, P., Bedford, T., Rambaut, A., Suchard, M. A., & Alekseyenko, A. V. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss084 · Cited by 1,145
Self-citationBeerli, P., & Felsenstein, J. (1999) · Genetics · doi:10.1093/genetics/152.2.763 · Cited by 986
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss086 · Cited by 974
Self-citationComparison of Bayesian and maximum-likelihood inference of population genetic parameters
Beerli, P. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti803 · Cited by 937
Bayesian inference of population size history from multiple loci
Heled, J., & Drummond, A. J. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-289 · Cited by 739
Self-citationAyres, D. L., Darling, A. E., Zwickl, D. J., Beerli, P., Holder, M. T., Lewis, P. O., Huelsenbeck, J. P., Ronquist, F., Swofford, D. L., Cummings, M. P., et al. (2011) · Systematic Biology · doi:10.1093/sysbio/syr100 · Cited by 707
Self-citationDensiTree: making sense of sets of phylogenetic trees
Bouckaert, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq110 · Cited by 704
Self-citationSmooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
Minin, V. N., Bloomquist, E. W., & Suchard, M. A. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn090 · Cited by 695
Self-citationPhylogeography Takes a Relaxed Random Walk in Continuous Space and Time
Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq067 · Cited by 687
Self-citationStadler, T., Kühnert, D., Bonhoeffer, S., & Drummond, A. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207965110 · Cited by 528
Self-citationVARIABLE SELECTION IN REGRESSION MODELS
Rao, M. S., & M.Venkataramanaih, M. S. (2013) · International Journal of Research in Commerce, IT and Management · Cited by 473
Many-core algorithms for statistical phylogenetics
Suchard, M. A., & Rambaut, A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp244 · Cited by 417
Self-citationvan de Laar, T., Pybus, O. G., Bruisten, S. M., Brown, D. J., Nelson, M. R., Bhagani, S., Vogel, M., Baumgarten, A., Chaix, M., Fisher, M., et al. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.02.006 · Cited by 318
Molecular phylogeny and evolution of primate mitochondrial DNA.
Hayasaka, K., Gojobori, T., & Horai, S. (1988) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040524 · Cited by 174
Kühnert, D., Stadler, T., Vaughan, T. G., & Drummond, A. J. (2014) · Journal of The Royal Society Interface · doi:10.1098/rsif.2013.1106 · Cited by 131
Self-citationWagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos
Alekseyenko, A. V., Lee, C. J., & Suchard, M. A. (2008) · Systematic Biology · doi:10.1080/10635150802434394 · Cited by 91
Self-citationEvolutionary Rates and Hbv: Issues of Rate Estimation with Bayesian Molecular Methods
Bouckaert, R., Alvarado-Mora, M. V., & Pinho, J. R. R. (2005) · Antiviral Therapy · doi:10.3851/imp2656 · Cited by 67
Self-citationA Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics
Vaughan, T. G., & Drummond, A. J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst057 · Cited by 60
Self-citationBayesian Selection of Nucleotide Substitution Models and Their Site Assignments
Wu, C., Suchard, M. A., & Drummond, A. J. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss258 · Cited by 48
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
ModelFinder: fast model selection for accurate phylogenetic estimates
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159
“2012), BEAST2 (Bouckaert et al. 2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al.”
MethodSelf-citationYu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. (2016) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12628 · Cited by 4,821
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556
Self-citationBayesian phylogenetic and phylodynamic data integration using BEAST 1.10
Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018) · Virus Evolution · doi:10.1093/ve/vey016 · Cited by 3,749
Self-citation
Metadata
- Authors
- Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J.
- Affiliations
- University of Auckland (NZ)
- University of California, Los Angeles (US)
- University of Edinburgh (GB)
- Corresponding author
- Bouckaert, Remco
- Drummond, Alexei J.
- ORCID
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-04-10
- Volume
- 10
- Issue
- 4
- Pages
- e1003537
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3985171
- OpenAlex
- W2026062398
- Cited by
- 6,527
- References
- 31
- Citations by year
- 2026: 364 · 2025: 464 · 2024: 509 · 2023: 492 · 2022: 588 · 2021: 745 · 2020: 801 · 2019: 784 · 2018: 724 · 2017: 484 · 2016: 302 · 2015: 213 · 2014: 44
- FWCI
- 131.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (publishedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ePrints Soton (University of Southampton) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- ResearchSpace (University of Auckland) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- National Science Foundation (1264153, 0856099)
- National Evolutionary Synthesis Center
- Wellcome Trust (095831)
- Royal Society
- Royal Society Te Apārangi
- National Institutes of Health
- National Human Genome Research Institute (R01HG006139)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- BEAST2, Bayesian phylogenetics, Markov chain Monte Carlo, package management, extensibility, phylodynamics, model averaging, substitution models, XML file format, open source software
- MeSH terms
- Bayes Theorem, Biological Evolution, Programming Languages, Software
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
