| TREEANNOTATOR2(1) | User Commands | TREEANNOTATOR2(1) |
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
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 |