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