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beauti2 - matches beast2-mcmc

BEAUTI2(1) User Commands BEAUTI2(1)

NAME

beauti2 - matches beast2-mcmc

SYNOPSIS

beauti2 -template [template file] -nex [nexus data file] -xmldat [beast xml file] -xml [beast file] -exitaction [writexml|usetemplate|usexml] -out [output file name] -capture -v -version -h -help

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 BEAUTI version matches BEAST2-MCMC.

OPTIONS

-template [template file] : BEAUti template to be used. Default templates/Standard.xml
-nex [nexus data file] : nexus file to be read using template, multiple -nex arguments are allowed
-xmldat [beast xml file] : as -nex but with BEAST 1 or 2 xml file instead of nexus file
-xml [beast file] : BEAST 2 XML file to be loaded
-exitaction [writexml|usetemplate|usexml] : what to do after processing arguments
-out [output file name] : file to be written
-capture : captures stdout and stderr and make them available under Help/Messages menu
-v, -version : print version
-h, -help : print this help message

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
May 2016 beauti2 2.4.1