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Network analysis
License and software

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

Stijn van Dongen, Graph Clustering by Flow Simulation, PhD thesis, University of Utrecht, May 2000.
( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm )

Stijn van Dongen, A cluster algorithm for graphs, Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000.
( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z )

Stijn van Dongen, Graph clustering via a discrete uncoupling process, Siam Journal on Matrix Analysis and Applications 30-1, p121-141, 2008.

Stijn van Dongen and Cei Abreu-Goodger, Using MCL to extract clusters from networks, in Bacterial Molecular Networks: Methods and Protocols, Methods in Molecular Biology, Vol 804, pages 281—295 (2012). PMID 22144159.

and add proper attributions to the MCL-edge home page http://micans.org/mcl/. 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).

The software is licensed under the GNU General Public License, version 3. It implies that the source code is available, and the license gives you the freedom to study the code and modify it in any way that you see fit. If you pass parts or all of the code, compiled parts of the code, or a derived product on to others, you have to make the code available to them on the same conditions. For more information about GNU software and the GNU philosophy go hither.

Download a a ready-to-install tarball containing the MCL-edge software. If you download e.g. mcl-12-068.tar.gz it can be installed as follows:

tar xzf mcl-12-068.tar.gz cd mcl-12-068 ./configure --prefix=$HOME/local make install

I am willing to consider different licensing terms. However, if you want to acquire additional rights beyond those granted by the GNU General Public License you must bear in mind that the software and its documentation represent well over a thousand hours of development. Decipher my contact page to get in touch.

Manual pages in html, troff, and ps are part of the distribution (and can be automatically installed), and they are also available from this site. Several other programs are part of the mcl distribution, they are described below.

Many thanks go to Joost van Baal who packages this mcl implementation for Debian and autofooled MCL. This implies that the tarball pointed to above should install on virtually any UNIX flavour.

The software is provided on an 'as is' basis. The implementation is fast (one of the aims in its design), and is grounded on a lean sparse matrix/vector architecture. It is command-line based and the source code documentation is also lean and sparse.