mcl-algorithm
The MCL (Markov Cluster Algorithm) is a fast and scalable cluster algorithm for graphs based on stochastic flow. The flow process employed by the algorithm 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 a wide range of sibling utilities for handling and analyzing graphs, matrices, and clusterings.
| Tags | Scientific/Engineering Bioinformatics Mathematics |
|---|---|
| Licenses | GPL |
| Operating Systems | Unix |
| Implementation | C |
Recent releases
- 05 Jun 2008 14:05
Changes: The mcl suite is moving towards a wider focus on general purpose large scale graph analysis, with the emphasis, besides clustering, on basic graph and clustering measures and transformations. The program mcxarray can now transform tabular gene expression data into graph input. The clm utility computes clustering coefficients, diameter and eccentricity, and betweenness centrality. Many fixes and improvements were made throughout.
- 24 Jan 2006 13:31
Changes: Numerous cleanups in much of the code. Improvements in caching intermediate results.
- 17 Nov 2005 14:41
Changes: mcl and a few of its sibling applications now accept a uniform transformation syntax to transform the values from either a label/value stream or an existing graph. Documentation of the various exchange formats was improved and gathered in the mcxio manual page.
- 11 Nov 2005 07:25
Changes: MCL can now read label input in a simple line-based format in which each line contains two labels and an optional value, separated by whitespace. Output clusters are returned as lines of tab-separated labels. The BLAST parser can stream this format directly to mcl, creating a concise and easy-to-manage sequence clustering pipeline.
- 30 Sep 2005 08:37
Changes: mcl now has better dump modes and iterand analysis capabilities to provide an easy interface with visualization programs. The BLAST module no longer requires the macro processor zoem by default, and many sibling analysis applications have received minor improvements.
