.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH BEAUTI2 "1" "May 2016" "beauti2 2.4.1" "User Commands"
.SH NAME
beauti2 \- matches beast2-mcmc
.SH SYNOPSIS
.B beauti2
\fB\-template\fR [template file] \fB\-nex\fR [nexus data file] \fB\-xmldat\fR [beast xml file]
\fB\-xml\fR [beast file] \fB\-exitaction\fR [writexml|usetemplate|usexml] \fB\-out\fR [output file name]
\fB\-capture\fR \fB\-v\fR \fB\-version\fR \fB\-h\fR \fB\-help\fR
.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 BEAUTI version matches BEAST2-MCMC.
.SH OPTIONS
.HP
\fB\-template\fR [template file] : BEAUti template to be used. Default templates/Standard.xml
.HP
\fB\-nex\fR [nexus data file] : nexus file to be read using template, multiple \fB\-nex\fR arguments are allowed
.HP
\fB\-xmldat\fR [beast xml file] : as \fB\-nex\fR but with BEAST 1 or 2 xml file instead of nexus file
.HP
\fB\-xml\fR [beast file] : BEAST 2 XML file to be loaded
.HP
\fB\-exitaction\fR [writexml|usetemplate|usexml] : what to do after processing arguments
.HP
\fB\-out\fR [output file name] : file to be written
.HP
\fB\-capture\fR : captures stdout and stderr and make them available under Help/Messages menu
.HP
\fB\-v\fR, \fB\-version\fR : print version
.HP
\fB\-h\fR, \fB\-help\fR : print this help message
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.