---
name: "treeannotator2"
section: "1"
platform: "linux"
package: "beast2-mcmc"
version: "2.7.6+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/treeannotator2"
---

# treeannotator2(1)

MCMC Output analysis of beast2 package

## NAME

treeannotator2 - MCMC Output analysis of beast2 package

## SYNOPSIS

**treeannotator** \[-heights \<keep\|median\|mean\|ca\>\] \[-burnin \<i\>\] \[-b \<i\>\] \[-limit \<r\>\] \[-target \<target\_file\_name\>\] \[-help\] \[-forceDiscrete\] \[-lowMem\] \[-hpd2D \<r\>\] \<input-file-name\> \[\<output-file-name\>\]

## 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 treeannotator version matches beast2-mcmc which is no new upstream version of beast-mcmc (1.x) but rather a rewritten version.

## OPTIONS

**-heights** an option of 'keep' (default), 'median', 'mean' or 'ca'

**-burnin** the percentage of states to be considered as 'burn-in'

**-b** the percentage of states to be considered as 'burn-in'

**-limit** the minimum posterior probability for a node to be annotated

**-target** specifies a user target tree to be annotated

**-help** option to print this message

**-forceDiscrete** forces integer traits to be treated as discrete traits.

**-lowMem** use less memory, which is a bit slower.

**-hpd2D** the HPD interval to be used for the bivariate traits

## EXAMPLES

-

  treeannotator2 test.trees out.txt

-

  treeannotator2 **-burnin** 10 **-heights** mean test.trees out.txt

-

  treeannotator2 **-burnin** 20 **-target** map.tree test.trees out.txt

## AUTHOR

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