The recommend citation for this software is:

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C-H., Xie, D., Suchard, MA., Rambaut, A., & Drummond, A. J. (2014). BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology, 10(4), e1003537. doi:10.1371/journal.pcbi.1003537

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

To cite previous versions of BEAST:

• 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
• 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 is:

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