Ubuntu Manpage: treeannotator2 - MCMC Output analysis of beast2 package

name
synopsis
description
options
examples
author

Provided by: beast2-mcmc_2.7.6+dfsg-1_all

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.