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Old 06-05-2008
mcl-algorithm 08-157 (Default branch)
The MCL (Markov Cluster Algorithm) is a fast andscalable cluster algorithm for graphs based onstochastic flow. The flow process employed by thealgorithm is mathematically sound andintrinsically tied to cluster structure in graphs,which is revealed as the imprint left by theprocess. The threaded implementation has handledgraphs of up to one million nodes within hours,and is widely used in the field of protein familyanalysis. It comes with a wide range of siblingutilities for handling and analyzing graphs,matrices, and clusterings.License: GNU General Public License (GPL)Changes:
The mcl suite is moving towards a wider focus ongeneral purpose large scale graph analysis, withthe emphasis, besides clustering, on basic graphand clustering measures and transformations. Theprogram mcxarray can now transform tabular geneexpression data into graph input. The clm utilitycomputes clustering coefficients, diameter andeccentricity, and betweenness centrality. Manyfixes and improvements were made throughout.Image

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LEARN ABOUT DEBIAN

mclindex

mclindex(7)							  MISCELLANEOUS 						       mclindex(7)

  NAME
      mclindex - a list of the utilities and modules present in the MCL distribution.

      For more information, consult mclfamily(7).

  Generic stuff
      mcl(1)
	the mcl manual page
      mclfaq(7)
	the mcl FAQ
      mcxio(5)
	the mcl matrix format specification
      mclpipeline(1)
	generic pipeline (parsing/matrix creation/clustering/display)
      mcx(1)
	interface to basic matrix operations
      mcxassemble(1)
	prepare input matrix from cooccurrence scores
      mcxdump(1)
	dump matrices, optionally map indices to labels
      mcxarray(1)
	transform array data to MCL matrices
      mcxconvert(1)
	convert between ascii/binary storage types

  Dealing with clustering results
      clmformat(1)
	display clusterings in browsable format
      clmdist(1)
	compute distances between clusterings
      clminfo(1)
	performance measures for clusterings
      clmmeet(1)
	compute intersection of clusterings
      clmmate(1)
	compute best matches between two clusterings
      clmimac(1)
	Interpret Matrices (c.q. MCL iterands) As Clusterings
      clmresidue(1)
	extend subgraph clusterings onto encompassing graph
      clmorder(1)
	reorder indices to represent blocks from different clusterings
      clmclose(1)
	fetch connected components from graphs or subgraphs

  Dealing with matrices
      mcxio(5)
	the mcl matrix format specification
      mcx(1)
	interface to basic matrix operations
      mcxsubs(1)
	extract submatrices by specifiying sets of nodes and clusters
      mcxmap(1)
	remap matrix indices / relabel graph nodes
      mcxassemble(1)
	prepare input matrix from cooccurrence scores

  Application specific parsers and wrappers

      BLAST package - Documentation only available if installed with --enable-blast
      __________________
      mclblastline(1)
	pipeline for clustering from blast files
      mcxdeblast(1)
	prepare input from blast files

  mclindex 12-068						      8 Mar 2012							 mclindex(7)