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.