If you use MCL 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 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 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 )
and proper attributions to mcl's home http://micans.org/mcl/. Do this also if you are using some wrapper around mcl such as the blast module. 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.
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 probably well over a thousand hours of development. Decipher my contact page to get in touch.