BEAST v1.4 2002-2006
        Bayesian Evolutionary Analysis Sampling Trees
                              by
             Alexei J. Drummond and Andrew Rambaut

                Department of Computer Science
                     University of Auckland
                    alexei@cs.auckland.ac.nz

              Institute of Evolutionary Biology
                    University of Edinburgh
                      a.rambaut@ed.ac.uk


Mac OS X (User-Interface) version README 
a.rambaut@ed.ac.uk - 31th Oct 2006

Contents:
1) INTRODUCTION
2) INSTALLING BEAST
3) CONVERTING SEQUENCES
4) RUNNING BEAST
5) ANALYZING RESULTS
6) SUPPORT & LINKS
7) ACKNOWLEDGMENTS 

___________________________________________________________________________
1) INTRODUCTION

BEAST (Bayesian evolutionary analysis sampling trees) is package for
evolutionary inference from molecular sequences.

BEAST uses a complex and powerful input format (specified in XML) to
describe the evolutionary model. This has advantages in terms of
flexibility in that the developers of BEAST do not have to try and predict
every analysis that researchers may wish to perform and explicitly provide
an option for doing it. However, this flexibility means it is possible to
construct models that don't perform well under the Markov chain Monte Carlo
(MCMC) inference framework used. We cannot test every possible model that
can be used in BEAST. There are two solutions to this: Firstly, we  supply
a range of recipes for commonly performed analyses that we know should work
in BEAST and provide example input files for these (although, the actual
data can also produce unexpected behavour). Secondly, we provide advice and
tools for the diagnosis of problems and suggestions on how to fix them:

<http://evolve.zoo.ox.ac.uk/beast/>
<http://evolve.zoo.ox.ac.uk/beast/help/>

BEAST is not a black-box into which you can put your data and expect an
easily interpretable answer. It requires careful inspection of the output
to check that it has performed correctly and usually will need tweaking,
adjustment and a number of runs to get a valid answer. Sorry.

___________________________________________________________________________
2) INSTALLING BEAST

The Mac OS X User-Interface version can be installed by simply dragging the
enclosing folder the location where you keep your applications. 

___________________________________________________________________________
3) CONVERTING SEQUENCES

A program called "BEAUti" will import data in NEXUS format, allow you to
select various models and options and generate an XML file ready for use in
BEAST.

To run BEAUti simply double-click the 'BEAUti v1.4' application icon.

___________________________________________________________________________
4) RUNNING BEAST

To run BEAUti simply double-click the 'BEAST v1.4' application icon.

You will be asked to select a BEAST XML input file.

For documentation on creating and tuning the input files look at the
documentation with in the doc/ folder or on-line at:

<http://evolve.zoo.ox.ac.uk/beast/help/>

___________________________________________________________________________
5) ANALYZING RESULTS

We have produced a powerful graphical program for analysing MCMC log files
(it can also analyse output from MrBayes and other MCMCs). This is called
'Tracer' and is available from the Tracer web site:

<http://evolve.zoo.ox.ac.uk/software/tracer>

Additionally, two new programs are distributed as part of the BEAST
package: LogCombiner & TreeAnnotator. LogCombiner can combine log or tree
files from multiple runs of BEAST into a single combined results file
(after removing appropriate burn-ins). TreeAnnotator can summarize a sample
of trees from BEAST using a single target tree, annotating it with
posterior probabilities, HPD node heights and rates. This tree can then be
viewed in a new program called 'FigTree' which is available from:

<http://evolve.zoo.ox.ac.uk/software/figtree>

___________________________________________________________________________
6) SUPPORT & LINKS

BEAST is a relatively new and extremely complex program and as such will
inevitably have bugs. Please email us to discuss any problems:

<alexei@cs.auckland.ac.nz>    - PLEASE NOTE THE NEW ADDRESS
<a.rambaut@ed.ac.uk>          - PLEASE NOTE THE NEW ADDRESS

We would encourage you to join the BEAST users' mailing-list to get
notifications of updates and bugs. At a later date this may be expanded to
be a discussion-list so that users can exchange ideas and help. You can
join the mailing list by sending an email to:

<beast-users-subscribe@googlegroups.com>

The website for beast is here:

<http://evolve.zoo.ox.ac.uk/beast/>

Source code distributed under the GNU Lesser General Public License:

<http://code.google.com/p/beast-mcmc/>

___________________________________________________________________________
7) ACKNOWLEDGMENTS

Thanks to the following for supplying code or assisting with the creation
or testing of BEAST:

    Roald Forsberg
    Simon Ho
    Philippe Lemey
    Gerton Lunter
    Sidney Markowitz
    Tulio de Oliveira
    Oliver Pybus
    Beth Shapiro
    Korbinian Strimmer
    Marc Suchard	

BEAST V1.4.1 has been released. To download: