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treeannotator2 - MCMC Output analysis of beast2 package


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>]


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.


-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


treeannotator2 test.trees out.txt
treeannotator2 -burnin 10 -heights mean test.trees out.txt
treeannotator2 -burnin 20 -target map.tree test.trees out.txt


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

May 2016 treeannotator2 2.4.1