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layout: site
title: Citation 
tags: [citation]
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		<p><br />
The recommend citation for this software is:</p>
<h2>BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis</h2>
<p><a href="https://doi.org/10.1371/journal.pcbi.1006650">
Bouckaert R., Vaughan T.G., Barido-Sottani J., Duchêne S., Fourment M., Gavryushkina A., et al. (2019) 
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology, 15(4), e1006650.</a></p>

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

<h6>To cite previous versions of BEAST:</h6>
<ul>
<li>Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C-H., Xie, D., Suchard, MA., Rambaut, A., &amp; 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 <em><a href="https://doi.org/10.1371/journal.pcbi.1003537" rel="nofollow">full text</a></em></li>
<li>Drummond AJ, Suchard MA, Xie D &amp; Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7 <em>Molecular Biology And Evolution</em> <strong>29</strong>: 1969-1973 <em><a class="external text" title="http://mbe.oxfordjournals.org/content/early/2012/02/25/molbev.mss075.abstract" href="http://mbe.oxfordjournals.org/content/29/8/1969" rel="nofollow">full text</a></em></li>
<li>Drummond AJ &amp; Rambaut A (2007) &#8220;BEAST: Bayesian evolutionary analysis by sampling trees.&#8221; <em>BMC Evolutionary Biology</em> <strong>7</strong>, 214 <a class="external text" title="http://www.biomedcentral.com/1471-2148/7/214/abstract" href="http://www.biomedcentral.com/1471-2148/7/214/abstract" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>To cite the phylogeographic model in BEAST:</h6>
<ul>
<li>Lemey P, Rambaut A, Drummond AJ &amp; Suchard MA (2009) <em>PLoS Computational Biology</em> <strong>5</strong>, e1000520. <a class="external text" title="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000520" href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000520" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>To cite the continuous trait model in BEAST:</h6>
<ul>
<li>Lemey P, Rambaut A, Welch JJ &amp; Suchard MA (2010) <em>Mol Biol Evol</em> <strong>27</strong>, 1877-1885. <a class="external text" title="http://mbe.oxfordjournals.org/content/27/8/1877" href="http://mbe.oxfordjournals.org/content/27/8/1877" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>To cite the relaxed clock model in BEAST:</h6>
<ul>
<li>Drummond AJ, Ho SYW, Phillips MJ &amp; Rambaut A (2006) <em>PLoS Biology</em> <strong>4</strong>, e88. <a class="external text" title="http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0040088" href="http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0040088" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>To cite the random local clock model in BEAST:</h6>
<ul>
<li>Drummond AJ &amp; Suchard MA (2010) <em>BMC Biology</em> <strong>8</strong>, 114. <a class="external text" title="http://www.biomedcentral.com/1741-7007/8/114" href="http://www.biomedcentral.com/1741-7007/8/114" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>To cite the Bayesian Skyline model in BEAST:</h6>
<ul>
<li>Drummond AJ, Rambaut A, Shapiro B &amp; Pybus OG (2005) <em>Mol Biol Evol</em> <strong>22</strong>, 1185-1192. <a class="external text" title="http://mbe.oxfordjournals.org/cgi/content/short/22/5/1185" href="http://mbe.oxfordjournals.org/cgi/content/short/22/5/1185" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>To cite the Bayesian Skyride model in BEAST:</h6>
<ul>
<li>Minin VN, Bloomquist EW &amp; Suchard MA (2008) <em>Mol Bio Evol</em>  <strong>25</strong>, 1459-1471. <a class="external text" title="http://mbe.oxfordjournals.org/content/25/7/1459" href="http://mbe.oxfordjournals.org/content/25/7/1459" rel="nofollow"><em>full text</em></a></li>
</ul>
<h6>The original phylogenetic MCMC paper is:</h6>
<ul>
<li>Drummond AJ, Nicholls GK, Rodrigo AG &amp; Solomon W (2002) <em>Genetics</em> <strong>161</strong>, 1307-1320. <em><a class="external text" title="http://www.genetics.org/cgi/content/full/161/3/1307" href="http://www.genetics.org/cgi/content/full/161/3/1307" rel="nofollow">full text</a></em></li>
</ul>