


  mclindex(7)               MISCELLANEOUS               mclindex(7)


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

      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



  mclindex 1.008, 09-308      4 Nov 2009                          1





  mclindex(7)               MISCELLANEOUS               mclindex(7)


      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 1.008, 09-308      4 Nov 2009                          2


