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 https://github.com/beast-dev/beast-mcmc/issues.

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.

BEAST 1.5.3                                        05/28/2010                                      BEAST-MCMC(1)