:tocdepth: 3

.. _rppr_pdprune:

=======
pdprune
=======

`pdprune` prunes the tree to maximize PD.

::

  usage: pdprune [options] tree

Options
=======

-o  Specify the filename to write to.
--out-dir  Specify the directory to write files to.
--prefix  Specify a string to be prepended to filenames.
--csv  Output the results as csv instead of a padded matrix.
--cutoff  Specify the maximum branch length to be trimmed.
--leaves  Specify the maximum number of leaves to leave un-trimmed.
--names-only  Only split out a list of names, rather than names and PD decrease.
--unsafe  Don't perform internal checks.
--never-prune-from  Provide a file containing sequence names that will not be pruned.
--never-prune-regex-from  Provide a file containing regular expressions; sequence names matching one of these will not be pruned.