NAME

       beast-mcmc - Bayesian evolutionary analysis sampling trees

SYNOPSIS

       beast-mcmc [OPTIONS] [input.xml]

       beast-mcmc [-verbose | -strict | -window | -options | -working | -seed | -errors i |
                  -threads i | -java | -beagle | -beagle_info | -beagle_resource_order | -help |
                  input.xml]

DESCRIPTION

       BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is
       orientated towards rooted, time-measured phylogenies inferred using strict or relaxed
       molecular clock models. It is intended both as a method of reconstructing phylogenies and
       as 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 suite of programs for analysing the
       results. There are three main areas of research for which the BEAUti/BEAST package is
       particularly applicable. These areas are species phylogenies for molecular dating,
       coalescent-based population genetics and measurably evolving populations (ancient DNA or
       time-stamped viral sequence data sets).

OPTIONS

       -verbose
           verbose XML parsing messages

       -strict
           fail on non conforming BEAST XML file

       -window
           provide a console window

       -options
           display an options dialog

       -working
           change working directory to input file´s directory

       -seed
           specify a random number generator seed

       -errors i
           maximum number of numerical errors before stopping

       -threads i
           the number of computational threads to use (default 1)

       -java
           use Java only, no native implementations

       -beagle
           use beagle library if available

       -beagle_info
           show information on available beagle resources

       -beagle_resource_order
           set order of beagle resources

       -help
           print usage screen

BUGS

       The BEAST bug tracking system can be found at
       http://code.google.com/p/beast-mcmc/issues/list.

SEE ALSO

       beauti(1).

REFERENCES

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

       •   Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.

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

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

AUTHORS

       Alexei J. Drummond
           Copyright holder for BEAST.

       Andrew Rambaut
           Copyright holder for BEAST.

       Marc A. Suchard
           Copyright holder for BEAST.

       Felix Feyertag <felix.feyertag@googlemail.com>
           Prepared this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       Copyright © 2002–2010 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST)
       Copyright © 2009–2010 Felix Feyertag (This manpage)

       The binaries and source code are made available and can be distributed subject to the
       following conditions:

       BEAST is Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed
       under the terms of the GNU Lesser General Public License. See the notice in individual
       files and the file LICENSE for licensing details.

       BEAST includes software libraries from projects whose licensing terms require that the
       following notices be included when they are distributed in binary form and that the
       recipient be given a copy of their respective licenses.

       •   This product includes software developed by the JDOM Project (http://www.jdom.org/)

       •   This product includes software developed by The Apache Software Foundation
           (http://www.apache.org/)

       •   The license for JDOM can be read in the LICENSE.txt file in the source distribution
           available at http://www.jdom.org/

       •   The license for the Commons Math library can be read at
           http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE.txt file in the source
           distribution available at http://jakarta.apache.org/commons/math/

       This manual page and its XML source can be used, modified, and redistributed as if it were
       in public domain.