Using MCL to extract clusters from networks

Abstract

MCL is a general purpose cluster algorithm for both weighted and unweighted networks. The algorithm utilises network topology as well as edge weights, is highly scalable and has been applied in a wide variety of bioinformatic methods. In this chapter, we give protocols and case studies for clustering of networks derived from, respectively, protein sequence similarities and gene expression profile correlations. © 2012 Springer Science+Business Media, LLC.