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.