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Citing BEAST and its models

The recommended citation for this program is:

  • Drummond AJ, Suchard MA, Xie D & Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology And Evolution 29: 1969-1973 full text

The previous citation of BEAST is:

  • Drummond AJ & Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7, 214 full text

To cite the phylogeographic model in BEAST:

  • Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Computational Biology 5, e1000520. full text

To cite the continuous trait model in BEAST:

  • Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol 27, 1877-1885. full text

To cite the relaxed clock model in BEAST:

  • Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88. full text

To cite the random local clock model in BEAST:

  • Drummond AJ & Suchard MA (2010) BMC Biology 8, 114. full text

To cite the Bayesian Skyline model in BEAST:

  • Drummond AJ, Rambaut A, Shapiro B & Pybus OG (2005) Mol Biol Evol 22, 1185-1192. full text

To cite the Bayesian Skyride model in BEAST:

  • Minin VN, Bloomquist EW & Suchard MA (2008) Mol Bio Evol  25, 1459-1471. full text

The original phylogenetic MCMC paper was:

  • Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320. full text

Note that BEAST uses models and techniques from a range of other publications which should be cited if possible.