beauti2(1)

Usage

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

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13