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'MCL' (Markov Cluster Algorithm) is a fast and scalable cluster algorithm for graphs based on stochastic flow. The flow process that the algorithm uses is mathematically sound and intrinsically tied to cluster structure in graphs, which is revealed as the imprint left by the process. The threaded implementation has handled graphs of up to one million nodes within hours, and is widely used in the field of protein family analysis. It comes with sibling utilities for handling and analyzing graphs, matrices, and clusterings.


User manpage available in HTML, PS format from; User FAQ available in HTML, PS format from


Download version 05-118 (stable)
released on 28 April 2005



LicenseVerified byVerified onNotes
GPLv2orlaterJanet Casey30 June 2005

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Stijn van Dongen Maintainer

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This entry (in part or in whole) was last reviewed on 30 June 2005.


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