README

   If you use MCL software in your research, cite it as you would cite a
   journal or a book. This includes papers published in regular or electronic
   journals, usage of MCL as a back-end to a database that is accessible via a
   web interface, or inclusion of MCL in a larger framework of software that is
   distributed for other people to use.  Include one of the following
   citations:

      Stijn van Dongen, Graph Clustering Via a Discrete Uncoupling Process,
      SIAM Journal on Matrix Analysis and Applications, 30(1):121-141, 2008.
      ( http://link.aip.org/link/?SJMAEL/30/121/1 )

      Stijn van Dongen, Graph Clustering by Flow Simulation.
      PhD thesis, University of Utrecht, May 2000.
      ( https://dspace.library.uu.nl/handle/1874/848 )

   and proper attributions to mcl's home http://micans.org/mcl/ and its author,
   Stijn van Dongen.  For biological applications, it is appropriate to cite,
   additionally, the reference article for the first application of mcl to
   biological data:

      Enright A.J., Van Dongen S., Ouzounis C.A.
      An efficient algorithm for large-scale detection of protein families,
      Nucleic Acids Research 30(7):1575-1584 (2002).
      ( https://pubmed.ncbi.nlm.nih.gov/11917018/ )

   The following article contain some practical recipes and examples that
   may be of interest:

      Stijn van Dongen, Cei Abreu-Goodger
      Using MCL to extract clusters from networks,
      in Bacterial Molecular Networks: Methods and Protocols,
      Methods in Molecular Biology, Vol 804, p281-295 (2012).
      ( http://www.ncbi.nlm.nih.gov/pubmed/22144159 )

   Please be advised that the TribeMCL module has been disabled.  With mcl's
   new label streaming facilities it is possible to cluster directly from BLAST
   files. Refer to the mcl website for examples.

   MCL documentation is in doc/, in various formats. It gets installed in
   <prefix>/share/doc/mcl/. A few example input graphs are in graphs/, in the
   mcl matrix format; these are installed in <prefix>/share/doc/mcl/examples/.
   The MCL webpage is at http://micans.org/mcl/ .

   The version tag, which is of the form dd-ddd, encodes the year and day in
   year in which the distribution was made. So 02-058 encodes the 58-th day of
   the year 2002.

Configure and compiler options

Synopsis

   configure options:
      --prefix=YOUR-PREFIX    (e.g. $HOME/local)
      --enable-blast

   By default, MCL is compiled using C ints and floats -- the ints are used to
   encode graph nodes/matrix indices, and the floats are used to encode edge
   weights / matrix entries.  These can be changed respectively to long and
   double, by adding '-DINDEX_AS_LONG', and/or '-DVALUE_AS_DOUBLE' to the
   CFLAGS environment variable.  The first enables a possibly wider range of
   indices to be used, the second increases the precision (which is presumably
   not useful in the vast majority of cases).  Using gcc under bash, you might
   for example do

      export CFLAGS='-g -O2 -Wall -ansi -pedantic -DVALUE_AS_DOUBLE'

   before doing ./configure and make. If you are rebuilding, make sure to do
   'make clean' first.  You need not use doubles though; MCL does fine with
   floats.  These features (changing the basic types) have not yet been tested
   thoroughly.

   For enabling rudimentary runtime integrity checks, add -DRUNTIME_INTEGRITY.

See also

   LICENSE for copyright and licensing, THANKS for contributors, INSTALL for
   generic installation instructions.