Using MCL to Extract Clusters from Networks

  • Stijn van DongenEmail author
  • Cei Abreu-Goodger
Part of the Methods in Molecular Biology book series (MIMB, volume 804)


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.

Key words

Network clustering Cluster analysis Protein sequence similarity Gene expression profiles 


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUK

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