beast2-mcmc(1)
Bayesian MCMC phylogenetic inference
Description
BEAST2-MCMC
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
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-window Provide a console window | |
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-options Display an options dialog | |
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-working Change working directory to input file’s directory | |
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-seed Specify a random number generator seed | |
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-prefix Specify a prefix for all output log filenames | |
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-statefile Specify the filename for storing/restoring the state | |
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-overwrite Allow overwriting of log files | |
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-resume Allow appending of log files | |
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-validate Parse the XML, but do not run -- useful for debugging XML | |
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-errors Specify maximum number of numerical errors before stopping | |
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-threads The number of computational threads to use (default 1), -1 for number of cores | |
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-java Use Java only, no native implementations | |
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-noerr Suppress all output to standard error | |
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-loglevel error,warning,info,debug,trace | |
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-instances divide site patterns amongst number of threads (use with -threads option) | |
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-beagle Use beagle library if available | |
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-beagle_info BEAGLE: show information on available resources | |
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-beagle_order BEAGLE: set order of resource use | |
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-beagle_CPU BEAGLE: use CPU instance | |
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-beagle_GPU BEAGLE: use GPU instance if available | |
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-beagle_SSE BEAGLE: use SSE extensions if available | |
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-beagle_single BEAGLE: use single precision if available | |
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-beagle_double BEAGLE: use double precision if available | |
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-beagle_scaling BEAGLE: specify scaling scheme to use | |
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-help Print this information and stop | |
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-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.