Provided by: beast2-mcmc_2.4.4+dfsg-1_all
beast2-mcmc - 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.