NAME

       beast2-mcmc - Bayesian MCMC phylogenetic inference

SYNOPSIS

       beast2-mcmc   [-window]   [-options]  [-working]  [-seed]  [-prefix  <PREFIX>]  [-statefile  <STATEFILE>]
       [-overwrite] [-resume] [-validate] [-errors <i>] [-threads  <i>]  [-java]  [-noerr]  [-loglevel  <LEVEL>]
       [-instances   <i>]   [-beagle]   [-beagle_info]   [-beagle_order   <order>]  [-beagle_CPU]  [-beagle_GPU]
       [-beagle_SSE] [-beagle_single] [-beagle_double] [-beagle_scaling  <default|none|dynamic|always>]  [-help]
       [-version] [<input-file-name>]

DESCRIPTION

       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. Included is a simple
       to  use  user-interface program for setting up standard analyses and a suit of programs for analysing the
       results.

       This is no new upstream version of beast-mcmc (1.x) but rather a rewritten version.

OPTIONS

       -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

       -prefix Specify a prefix for all output log filenames

       -statefile Specify the filename for storing/restoring the state

       -overwrite Allow overwriting of log files

       -resume Allow appending of log files

       -validate Parse the XML, but do not run -- useful for debugging XML

       -errors Specify maximum number of numerical errors before stopping

       -threads The number of computational threads to use (default 1), -1 for number of cores

       -java Use Java only, no native implementations

       -noerr Suppress all output to standard error

       -loglevel error,warning,info,debug,trace

       -instances divide site patterns amongst number of threads (use with -threads option)

       -beagle Use beagle library if available

       -beagle_info BEAGLE: show information on available resources

       -beagle_order BEAGLE: set order of resource use

       -beagle_CPU BEAGLE: use CPU instance

       -beagle_GPU BEAGLE: use GPU instance if available

       -beagle_SSE BEAGLE: use SSE extensions if available

       -beagle_single BEAGLE: use single precision if available

       -beagle_double BEAGLE: use double precision if available

       -beagle_scaling BEAGLE: specify scaling scheme to use

       -help Print this information and stop

       -version Print version and stop

EXAMPLES

              beast2-mcmc test.xml

              beast2-mcmc -window test.xml

              beast2-mcmc -help

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

beast2-mcmc 2.4.1                                   May 2016                                      BEAST2-MCMC(1)