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Table 1 Main features of the graph clustering approaches presented in this study.

From: Evaluation of clustering algorithms for protein-protein interaction networks

  Restricted Neighborhood Search Clustering (RNSC) Markov Clustering (MCL) Molecular Complex Detection (MCODE) Super-paramagnetic clustering (SPC)
Type Local search cost based Flow simulation Local neighbourhood density search Hierarchical
Allow multiple assignations No No Yes No
Allow unassigned nodes No No Yes No
Edge-weighted graphs supported No Yes No Yes
First application Protein complex prediction Protein family detection Protein complex detection  
Other applications / Identification of ortholog groups, protein complexes, peer-to-peer node clustering, image retrieval, Word Sense Discrimination, molecular pathway discovery, structural domains, ... / Image clustering, microarray data clustering, protein complexes detection, protein structure classification, identification of ortholog groups, ...
Availability Upon request http://micans.org/mcl/ ftp://ftp.blueprint.org/pub/BIND/README Upon request
Developper King AD Van Dongen S Bader GD and Hogue CWV Blatt M, Wiseman S, Domany E
References [21] [35] [19] [18]