  Summary: Most cellular tasks are performed not by individual proteins, but by
groups of functionally associated proteins, often referred to as modules. In a
protein assocation network modules appear as groups of densely interconnected
nodes, also called communities or clusters. These modules often overlap with
each other and form a network of their own, in which nodes (links) represent
the modules (overlaps). We introduce CFinder, a fast program locating and
visualizing overlapping, densely interconnected groups of nodes in undirected
graphs, and allowing the user to easily navigate between the original graph and
the web of these groups. We show that in gene (protein) association networks
CFinder can be used to predict the function(s) of a single protein and to
discover novel modules. CFinder is also very efficient for locating the cliques
of large sparse graphs.
  Availability: CFinder (for Windows, Linux, and Macintosh) and its manual can
be downloaded from http://angel.elte.hu/clustering.
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