treeannotator2 - MCMC Output analysis of beast2 package

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

treeannotator2 2.4.1                                May 2016                                   TREEANNOTATOR2(1)

       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.

              treeannotator2 test.trees out.txt

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

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

       treeannotator2 - MCMC Output analysis of beast2 package

-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

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>]