:tocdepth: 3

.. _rppr_min_adcl:

========
min_adcl
========

`min_adcl` finds a good collection of sequences to cut from a placefile's ref tree.

::

  usage: min_adcl [options] placefile

Options
=======

--point-mass  Treat every pquery as a point mass concentrated on the highest-weight placement.
--pp  Use posterior probability for the weight.
-c  Reference package path.
-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.
--leaf-mass  Fraction of mass to be distributed uniformly across leaves. Default 0.

Details
=======

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

Chooses the set of *k* sequences *X* that minimize the average distance between each placement the closest sequence in *X*.

You can read more in the announcement_ or the paper_.

See :ref:`min_adcl_tree <rppr_min_adcl_tree>` for the same equivalent operation on a tree without placements.

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