:tocdepth: 3

.. _guppy_mcl:

===
mcl
===

`mcl` cluster pqueries using Markov clustering via MCL.

::

  usage: mcl [options] placefile

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.
--pp  Use posterior probability for the weight.
--inflation  If specified, pass this as the inflation value to MCL.

Details
=======

Markov clustering done via the Markov Clustering Library `MCL`_ on the overlap graph (see the :doc:`guppy_ograph` documentation for information about the overlap graph).

.. _MCL: http://micans.org/mcl/