.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH BEAST2-MCMC "1" "May 2016" "beast2-mcmc 2.4.1" "User Commands"
.SH NAME
beast2-mcmc \- Bayesian MCMC phylogenetic inference
.SH SYNOPSIS
.B 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>]
.SH 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.
.P
This is no new upstream version of beast-mcmc (1.x) but rather a rewritten
version.
.SH OPTIONS
.HP
\fB\-window\fR Provide a console window
.HP
\fB\-options\fR Display an options dialog
.HP
\fB\-working\fR Change working directory to input file's directory
.HP
\fB\-seed\fR Specify a random number generator seed
.HP
\fB\-prefix\fR Specify a prefix for all output log filenames
.HP
\fB\-statefile\fR Specify the filename for storing/restoring the state
.HP
\fB\-overwrite\fR Allow overwriting of log files
.HP
\fB\-resume\fR Allow appending of log files
.HP
\fB\-validate\fR Parse the XML, but do not run \fB\-\-\fR useful for debugging XML
.HP
\fB\-errors\fR Specify maximum number of numerical errors before stopping
.HP
\fB\-threads\fR The number of computational threads to use (default 1), \fB\-1\fR for number of cores
.HP
\fB\-java\fR Use Java only, no native implementations
.HP
\fB\-noerr\fR Suppress all output to standard error
.HP
\fB\-loglevel\fR error,warning,info,debug,trace
.HP
\fB\-instances\fR divide site patterns amongst number of threads (use with \fB\-threads\fR option)
.HP
\fB\-beagle\fR Use beagle library if available
.HP
\fB\-beagle_info\fR BEAGLE: show information on available resources
.HP
\fB\-beagle_order\fR BEAGLE: set order of resource use
.HP
\fB\-beagle_CPU\fR BEAGLE: use CPU instance
.HP
\fB\-beagle_GPU\fR BEAGLE: use GPU instance if available
.HP
\fB\-beagle_SSE\fR BEAGLE: use SSE extensions if available
.HP
\fB\-beagle_single\fR BEAGLE: use single precision if available
.HP
\fB\-beagle_double\fR BEAGLE: use double precision if available
.HP
\fB\-beagle_scaling\fR BEAGLE: specify scaling scheme to use
.HP
\fB\-help\fR Print this information and stop
.HP
\fB\-version\fR Print version and stop
.SH EXAMPLES
.IP
beast2-mcmc test.xml
.IP
beast2-mcmc \fB\-window\fR test.xml
.IP
beast2-mcmc \fB\-help\fR
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.