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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)
Clustering or not