Questions about the clustering algorithm MCL may be answered in the mcl FAQ. For other questions please subscribe to the mcl-users mailing list at http://listserver.ebi.ac.uk/mailman/listinfo/mcl-users. I may respond to queries sent to me in private, but as I get quite a few of these I prefer to have a public forum that is archived. By posting your question in a publicly accessible forum you are helping other people that may have similar enquiries.
Alternatively, it is alright if you do not subscribe, but e-mail me directly at stijn (at) ebi (dot) ac (dot) uk. I will then send a copy of all my replies to aforementioned mailing list. This list is low-traffic. Currently it is not a community forum but rather a place for archival and referal of queries and their answers. Additionally, the list is used for announcements of releases, for bug reports, and for other mcl-related matters.
When seeking help regarding running or compiling one of the MCL-edge programs, remember to describe the problem as clearly as possible. This includes (whether it concerns compiling mcl or running mcl programs) a full description of what you did (i.e. the command line statements), what you expected, and what happened (i.e. the screen output or a concise description or example of unexpected contents found in files). Do try to make examples as small as possible. Do not paste or attach files but rather use excerpts that demonstrate the issue at hand.