We can migrate some of the content from the MCODE site here: http://cbio.mskcc.org/~bader/software/mcode/
MCODE Cytoscape PlugIn
The MCODE Cytoscape PlugIn finds clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.
MCODE is a relatively fast method of clustering, although it does not currently provide any statistical score on the resulting clusters. It can be used as discovery tool when analyzing a network. See the paper for more information.
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