MCL algorithm comparison

Brohee and van Helden 2006, BMC [BH06]

BH06 compared Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Super Paramagnetic Clustering (SPC), and Molecular Complex Detection (MCODE), using annotated protein complex as bench mark. Random noises were introduced by randomly adding and deleting edges. MCL is the most reliable and robust method. 

disconnected clusters from MCL

Our MCL clusters at high I-values give genes in clusters with disconnected nodes. This is a problem has been discussed before:

http://larsjuhljensen.wordpress.com/2010/03/01/analysis-markov-clustering-and-the-case-of-the-unnatural-clusters/

According to the post, this is not an "error", but a possible though "unexpected" result. Looks like "--force-connected=y" option might solve this problem. I will redo the clustering and then check.