BEAST: Bayesian evolutionary analysis by sampling trees

BMC Evolutionary Biology
Alexei J Drummond, Andrew Rambaut

Abstract

The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

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Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Vladimir N Minin, Marc A Suchard
Jan 6, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Susanne S Renner, Hanno Schaefer
May 5, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Trevor D Price
May 19, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Giusi AmoreTony L Goldberg
Sep 22, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Anne C StoneSudhir Kumar
Nov 3, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Russell D GraySimon J Greenhill
Mar 2, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Russell D GraySimon J Greenhill
Aug 17, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Ben CollenNick J B Isaac
Jan 11, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·J N YoungDmitry Filatov
May 30, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Terry J Ord, Joan Garcia-Porta
Jan 11, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter J FranksDavid J Beerling
Feb 6, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tanja Stadler, Sebastian Bonhoeffer
Feb 6, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Richard J OrtonDaniel T Haydon
Aug 14, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Rebecca R GrayOliver G Pybus
May 4, 2012·Cold Spring Harbor Perspectives in Medicine·Sten H Vermund, Andrew J Leigh-Brown
Dec 15, 2010·Genome Research·Ellen D GunnarsdóttirMark Stoneking
Jul 20, 2010·The Plant Cell·Terezie MandákováMartin A Lysak
Feb 11, 2012·Biological Reviews of the Cambridge Philosophical Society·Lorraine Michelet, Catherine Dauga
Nov 11, 2011·Conservation Biology : the Journal of the Society for Conservation Biology·Dorothea V PioNicolas Salamin
Jul 16, 2010·Transboundary and Emerging Diseases·M HabielaD J Paton
Jul 18, 2009·Science·Adrian W BriggsSvante Pääbo
May 13, 2009·Science·Christophe FraserWHO Rapid Pandemic Assessment Collaboration
Apr 8, 2010·Science Translational Medicine·David M ButlerDavey M Smith
Jul 27, 2010·Applied and Environmental Microbiology·Henk C den BakkerMartin Wiedmann
Jan 20, 2012·Journal of Clinical Microbiology·P BassetD S Blanc
Dec 14, 2011·Journal of Clinical Microbiology·Zhen ZhuWenbo Xu
Apr 16, 2010·Journal of Clinical Microbiology·Sanela SvrakaMarion Koopmans
Jul 13, 2012·Journal of Virology·Virginie SauvageMarc Eloit
Jul 16, 2010·Journal of Virology·Maria GullbergA Michael Lindberg
May 20, 2011·Journal of Virology·Edward C HolmesINSIGHT FLU002 Study Group
Jul 1, 2011·Journal of Virology·Denali BoonKarin Bok
Sep 28, 2012·Journal of Virology·Marcio R T NunesPedro F C Vasconcelos
Jul 16, 2010·Journal of Virology·Albert J AugusteChristine V F Carrington
Nov 18, 2011·Journal of Virology·Xian-Dan LinYong-Zhen Zhang
May 25, 2012·Journal of Virology·Rebecca R GrayMarco Salemi
Jun 24, 2011·Journal of Virology·Xiao-Ling PanGuodong Liang
Sep 18, 2009·Journal of Virology·Karin BokKim Y Green
Sep 21, 2012·Journal of Virology·Jeremy HuynhEric F Donaldson
Oct 2, 2009·Journal of Virology·Ana B AbecasisPhilippe Lemey
Jul 20, 2012·Journal of Virology·Michael A Purdy
Oct 31, 2008·Journal of Virology·Oliver G PybusPaul Klenerman
Sep 18, 2009·Journal of Virology·Peter J KerrEdward C Holmes
Jan 23, 2009·Journal of Virology·Stéphane HuéUK Collaborative Group on HIV Drug Resistance
Nov 6, 2009·Journal of Virology·Amadou Alpha SallEdward C Holmes
Feb 11, 2011·Journal of Virology·Eva DörrschuckRalf R Tönjes
Nov 28, 2008·Journal of Virology·Zigui ChenRobert D Burk
Dec 19, 2008·Journal of Virology·E C McWilliam LeitchPeter Simmonds
Apr 9, 2010·Journal of Virology·Israel Pagan, Edward C Holmes
Jan 22, 2010·Journal of Virology·Hurng-Yi WangDing-Shinn Chen
Feb 13, 2009·Journal of Virology·Mark J SchreiberMartin L Hibberd
Dec 14, 2012·Journal of Virology·Melissa J WardAndrew J Leigh Brown
May 27, 2011·Journal of Virology·Allison L Hicks, Siobain Duffy
Mar 20, 2009·Journal of Virology·Eleca J DunhamJeffery K Taubenberger
Mar 25, 2011·Journal of Virology·Pablo R MurciaEdward C Holmes
Jan 18, 2013·Journal of Virology·Jackie E MaharCarl D Kirkwood
Dec 21, 2012·Journal of Virology·Serena A CarrollStuart T Nichol
Mar 29, 2013·Journal of Virology·John-Sebastian EdenPeter A White
Sep 2, 2011·Journal of Virology·Amit KapoorW Ian Lipkin
Nov 25, 2011·Journal of Virology·Jayna RaghwaniOliver G Pybus
Nov 11, 2011·Journal of Virology·Andrew B AllisonColin R Parrish
Jun 14, 2013·MBio·Anne KoppSandra Junglen
May 31, 2012·Molekuliarnaia biologiia·E L Subbotina, V B Loktev
Dec 13, 2012·Genome Génome / Conseil National De Recherches Canada·Filipe de Carvalho VictoriaAntônio Costa de Oliveira
Dec 8, 2009·Annual Review of Entomology·Fredrik Ronquist, Andrew R Deans
Dec 15, 2010·Interdisciplinary Perspectives on Infectious Diseases·Eamon B O'Dea, Claus O Wilke
Mar 11, 2010·Cytogenetic and Genome Research·Todd A CastoeDavid D Pollock
Sep 7, 2013·Veterinary Research·Begoña Valdazo-GonzálezDonald P King
Oct 27, 2010·BMC Bioinformatics·Elena E GiorgiTanmoy Bhattacharya
Jan 7, 2010·BMC Bioinformatics·Ben C Stöver, Kai F Müller
Jan 26, 2011·BMC Bioinformatics·Martin O JonesMark L Blaxter
Dec 15, 2011·BMC Bioinformatics·Fernando Izquierdo-CarrascoAlexandros Stamatakis
Apr 23, 2010·BMC Evolutionary Biology·Małgorzata PilotElena Tsingarska
Jun 8, 2010·BMC Evolutionary Biology·Thomas DatzmannFrieder Mayer
Jun 23, 2010·BMC Evolutionary Biology·Katarzyna Bozek, Thomas Lengauer
Jun 23, 2010·BMC Evolutionary Biology·Katherine J BrownJulia J Day
Aug 14, 2010·BMC Evolutionary Biology·Albert N MenezesHector N Seuánez
Sep 3, 2010·BMC Evolutionary Biology·Tommi NymanJean-Luc Boevé
Jan 30, 2010·BMC Evolutionary Biology·Ignacio RiberaAlexandra Cieslak
Sep 24, 2010·BMC Evolutionary Biology·Jessica E LightDavid L Reed
Feb 2, 2010·BMC Evolutionary Biology·Akira KatoShigehisa Hirose