Main Page

From BEAST Software

Jump to: navigation, search

Contents

What is BEAST?

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

What can BEAST do?

New! We now have a short paper describing BEAST which can be used as a citation

New! How do I do model comparison?

New! How do tree prior distributions affect estimation of rates and dates?

New! How do you summarize the posterior distribution of trees?

Downloads

BEAST v1.5.2 has been released

9th October 2009: What's new in this version?

Tracer v1.4.1 has been released

Downloadable Practicals with Data

Divergence Dating (Primates) v1.0.zip
Estimating a date of divergence using fossil calibration for primates.
Divergence Dating (Papillomaviruses) v1.0.zip
Estimating a date of divergence using a host co-divergence for feline papillomaviruses (similar to the primate practical but virus-orientated).
Estimating Rates in Viruses (RSVA) v1.0.zip
Estimating the rate of evolution from serially-sampled sequences (dated tips) using an RSVA (human respiratory syncytial virus subgroup A) data set.
Combined Practical (Viruses) v1.0.zip
A three-part virus practical that covers the same material as the two above but has an additional part on Bayesian Skyline Plots.

A Rough Guide to BEAST 1.4

Mailing List

Users are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.

Send an email to beast-users-subscribe@googlegroups.com or go to the mailing list site:

http://groups.google.com/group/beast-users

Getting started

These tutorials use the graphical applications of BEAST to perform analyses using the provided example files:

We now have a BEAST manual for download as a single PDF file:

Citing BEAST

The recommended citation for this program is:

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

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

The original MCMC paper was:

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

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

Contents of this website

BEAST Developers

The complete source code for BEAST is now distributed under the GNU Lesser General Public License and the source code, bug tracking database and information for developers is now hosted by Google:

http://beast-mcmc.googlecode.com/

Phylogenetic Bayesian MCMC Trials

This is the beginnings of a site devoted to creating a set of comparisons between different programs that perform Bayesian MCMC phylogenetics. The aim is to identify where these programs overlaps in terms of the models they implement and to provide data sets that can be used to test these models. This will allow us to cross-validate programs using independent implementations of the same models and to compare the efficiency of different sampling strategies.

Phylogenetic Bayesian MCMC Trials

Alexei Drummond and Andrew Rambaut
Copyright © 2002-2007 All rights reserved.

Retrieved from "http://beast.bio.ed.ac.uk/Main_Page"
Personal tools