:tocdepth: 3

.. _rppr_min_adcl_tree:

=============
min_adcl_tree
=============

`min_adcl_tree` finds a good collection of sequences to cut from a tree.

::

  usage: min_adcl_tree [options] newick.tre

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.
--no-csv  Output the results as a padded matrix instead of csv.
--node-numbers  Put the node numbers in where the bootstraps usually go.
--seed  Set the random seed, an integer > 0. Default is 1.
-v  If specified, write progress output to stderr.
-t  If specified, the path to write the trimmed tree to.
--leaves  The maximum number of leaves to keep in the tree.
--max-adcl  The maximum ADCL that a solution can have.
--algorithm  Which algorithm to use to prune leaves. Choices are 'greedy', 'full', 'force', and 'pam'. Default full.
--all-adcls-file  If specified, write out a csv file containing every intermediate computed ADCL.
--log  If specified with the full algorithm, write out a csv file containing solutions at every internal node.
--always-include  If specified, the leaf names read from the provided file will not be trimmed.
--query-seqs  A comma-separated list of leaves to turn into query sequences.

Details
=======

.. important::
  ``rppr min_adcl_tree`` Prints the labels of the leaves that should be **removed** from the tree, not those that should be kept.

``min_adcl_tree`` chooses the set of *k* sequences *X* that minimize the average distance from each pruned sequence to the closest sequence in *X*.

You can read more in the announcement_ or the paper_.

See :ref:`min_adcl_tree <rppr_min_adcl>` for the same equivalent operation on a tree with placements.

.. _announcement: http://matsen.fhcrc.org/general/2012/05/31/adcl-paper.html
.. _paper: http://arxiv.org/abs/1205.6867