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beauti readme

By Jessica Green,2014-10-15 14:55
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beauti readme

     BEAUti v1.4.7 2002-2008

     Bayesian Evolutionary Analysis Utility

     by

     Andrew Rambaut AND Alexei J. Drummond

     Institute of Evolutionary Biology

     University of Edinburgh

     a.rambaut@ed.ac.uk

     Department of Computer Science

     University of Auckland

     alexei@cs.auckland.ac.nz

UNIX / Mac OS X / Linux / Windows README

    Last updated: a.rambaut@ed.ac.uk - 1st February 2008

Contents:

    1) INTRODUCTION

    2) INSTALLING AND RUNNING BEAUTI

    3) DOCUMENTATION

    4) SUPPORT & LINKS

    5) ACKNOWLEDGMENTS

    ___________________________________________________________________________ 1) INTRODUCTION

    BEAUti (Bayesian Evolutionary Analysis Utility - apologies for the poor acronym) is a simple user interface for creating input files to run BEAST. It takes sequence data as NEXUS format (as used by PAUP and MrBayes), allows you to select the evolutionary model, tune the operators and configure the MCMC. Then it generates an XML format file that can be used with BEAST.

BEAST - <http://beast.bio.ed.ac.uk/>

PAUP - <http://paup.csit.fsu.edu/>

    MrBayes - <http://morphbank.ebc.uu.se/mrbayes/>

    Note that this program cannot create even a small fraction of the models that are potentially available in BEAST. It does however provide an easy way to set up some of the simpler and more commonly used ones. It can also provide a way to generate the input XML format for subsequent editing and tweaking.

    ___________________________________________________________________________ 2) INSTALLING AND RUNNING BEAUTI

    Mac OS X: To install BEAUti, simply drag the program file to where you normally put applications. Then double click to run.

    Windows : Copy or move the folder to where you normally put applications and then double click the "BEAUti v1.4.7.exe" file to run.

    Linux / UNIX : Copy or move the folder to where you normally put applications and then double click the "beauti.jar" file to run.

    If double-clicking the file "beauti.jar" expands the archive into some directories/folders then Java may not be correctly installed. Try typing:

java -version

    at a command-line prompt. This should return the version number of the Java installed. If the version is older than 1.4 or you just get an error message, you will need to install the latest version of Java:

<http://java.sun.com/>

    If Java is correctly installed you should also be able to run BEAUTi by typing:

java -jar beauti.jar

    ___________________________________________________________________________ 3) DOCUMENTATION

The latest manual can be downloaded from here:

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

    ___________________________________________________________________________ 4) SUPPORT & LINKS

Please email us to discuss any problems:

<a.rambaut@ed.ac.uk>

    <alexei@cs.auckland.ac.nz>

    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 here:

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

The website for beast is here:

<http://beast.bio.ed.ac.uk/>

    Source code distributed under the GNU Lesser General Public License:

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

    ___________________________________________________________________________ 5) ACKNOWLEDGMENTS

    Thanks to the following for supplying code or assisting with the creation or testing of BEAST and its associated software:

     Michael Defoin Platel

     Roald Forsberg

     Joseph Heled

     Simon Ho

     Philippe Lemey

     Gerton Lunter

     Sidney Markowitz

     Tulio de Oliveira

     Oliver Pybus

     Beth Shapiro

     Korbinian Strimmer

     Marc Suchard

     + numerous other users who have kindly helped make BEAST better.

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