.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH TREEANNOTATOR2 "1" "May 2016" "treeannotator2 2.4.1" "User Commands"
.SH NAME
treeannotator2 \- MCMC Output analysis of beast2 package
.SH SYNOPSIS
.B treeannotator
[\-heights <keep|median|mean|ca>] [\-burnin <i>] [\-b <i>] [\-limit <r>] [\-target <target_file_name>] [\-help] [\-forceDiscrete] [\-lowMem] [\-hpd2D <r>] <input\-file\-name> [<output\-file\-name>]
.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 treeannotator version matches beast2-mcmc which is no new upstream version of beast-mcmc (1.x) but rather a rewritten
version.
.SH OPTIONS
.HP
\fB\-heights\fR an option of 'keep' (default), 'median', 'mean' or 'ca'
.HP
\fB\-burnin\fR the percentage of states to be considered as 'burn\-in'
.HP
\fB\-b\fR the percentage of states to be considered as 'burn\-in'
.HP
\fB\-limit\fR the minimum posterior probability for a node to be annotated
.HP
\fB\-target\fR specifies a user target tree to be annotated
.HP
\fB\-help\fR option to print this message
.HP
\fB\-forceDiscrete\fR forces integer traits to be treated as discrete traits.
.HP
\fB\-lowMem\fR use less memory, which is a bit slower.
.HP
\fB\-hpd2D\fR the HPD interval to be used for the bivariate traits
.SH EXAMPLES
.IP
treeannotator2 test.trees out.txt
.IP
treeannotator2 \fB\-burnin\fR 10 \fB\-heights\fR mean test.trees out.txt
.IP
treeannotator2 \fB\-burnin\fR 20 \fB\-target\fR map.tree test.trees out.txt
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.