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Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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Drummond, Alexei J., Suchard, Marc A., Xie, Dong, Rambaut, Andrew·2012·Molecular Biology and Evolution
DOI 10.1093/molbev/mss075
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Abstract

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk.

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Research works printed but not linked: 22

  1. Alekseyenko, 2008, Wagner and Dollo: a stochastic duet by composing two parsimonious solos, Syst Biol., 57, 772, 10.1080/10635150802434394 · DOI
  2. Ayres, 2011, BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics, Syst Biol., 61, 170, 10.1093/sysbio/syr100 · DOI · Paper page
  3. Bielejec, 2011, Spread: spatial phylogenetic reconstruction of evolutionary dynamics, Bioinformatics, 27, 2910, 10.1093/bioinformatics/btr481 · DOI
  4. Bloomquist, 2010, Unifying vertical and nonvertical evolution: a stochastic ARG-based framework, Syst Biol., 59, 27, 10.1093/sysbio/syp076 · DOI
  5. Drummond, 2007, Beast: Bayesian evolutionary analysis by sampling trees, BMC Evol Biol., 7, 214, 10.1186/1471-2148-7-214 · DOI · Paper page
  6. Heled, 2008, Bayesian inference of population size history from multiple loci, BMC Evol Biol., 8, 289, 10.1186/1471-2148-8-289 · DOI · Paper page
  7. Heled, 2011, Calibrated tree priors for relaxed phylogenetics and divergence time estimation, Syst Biol., 61, 138, 10.1093/sysbio/syr087 · DOI · Paper page
  8. Lemey, 2009, Bayesian phylogeography finds its roots, PLoS Comput Biol., 5, e1000520, 10.1371/journal.pcbi.1000520 · DOI
  9. Lemey, 2010, Phylogeography takes a relaxed random walk in continuous space and time, Mol Biol Evol., 27, 1877, 10.1093/molbev/msq067 · DOI · Paper page
  10. Li, 2012, Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics, Mol Biol Evol., 29, 751, 10.1093/molbev/msr232 · DOI
  11. McCormack, 2011, Calibrating divergence times on species trees versus gene trees: implications for speciation history of aphelocoma jays, Evolution, 65, 184, 10.1111/j.1558-5646.2010.01097.x · DOI · Paper page
  12. Minin, 2008, Counting labeled transitions in continuous-time Markov models of evolution, J Math Biol., 56, 391, 10.1007/s00285-007-0120-8 · DOI · Paper page
  13. Minin, 2008, Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics, Mol Biol Evol., 25, 1459, 10.1093/molbev/msn090 · DOI · Paper page
  14. O'Brien, 2009, Learning to count: robust estimates for labeled distances between molecular sequences, Mol Biol Evol., 26, 801, 10.1093/molbev/msp003 · DOI
  15. Rambaut, 2009, Accommodating the effect of ancient DNA damage on inferences of demographic histories, Mol Biol Evol., 26, 245, 10.1093/molbev/msn256 · DOI
  16. Sato, 1999, Phylogeny of Darwin's finches as revealed by mtDNA sequences, Proc Natl Acad Sci U S A., 96, 5101, 10.1073/pnas.96.9.5101 · DOI
  17. Shapiro, 2011, A Bayesian phylogenetic method to estimate unknown sequence ages, Mol Biol Evol., 28, 879, 10.1093/molbev/msq262 · DOI
  18. Stadler, 2010, Sampling-through-time in birth–death trees, J Theor Biol., 267, 396, 10.1016/j.jtbi.2010.09.010 · DOI
  19. Suchard, 2009, Many-core algorithms for statistical phylogenetics, Bioinformatics, 25, 1370, 10.1093/bioinformatics/btp244 · DOI · Paper page
  20. Suchard, 2003, Hierarchical phylogenetic models for analyzing multipartite sequence data, Syst Biol., 52, 649, 10.1080/10635150390238879 · DOI
  21. Sulloway, 1982, The Beagle collections of Darwin's finches (Geospizinae), Bull Br Mus., 43, 49
  22. Wu, 2011, Joint inference of microsatellite mutation models, population history and genealogies using trans-dimensional MCMC, Genetics, 188, 151, 10.1534/genetics.110.125260 · DOI

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Metadata

Authors
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A.
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2012-02-25
Volume
29
Issue
8
Pages
1969-1973
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/molbev/mss075
OpenAlex
W2130362098
Cited by
10,063
References
2
FWCI
262.43
Type
journal article
Language
en
Open access
hybrid

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