beast2-mcmc(1) Bayesian MCMC phylogenetic inference


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>]


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.


-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


beast2-mcmc test.xml
beast2-mcmc -window test.xml
beast2-mcmc -help


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