


  mcl(7)                    MISCELLANEOUS                    mcl(7)


  NAME
      mclfamily - a description of the mcl family of cluster applications.

      mcl  is an implementation of the Markov Cluster Algorithm, aka MCL algo-
      ritm.  It is described in the mcl manual.   Several  other  applications
      are part of the MCL distribution. This manual pages gives an overview.

  DESCRIPTION
      mcl(1)         the cluster algorithm
      mclfaq(7)      MCL Frequently Asked Questions
      mcxio(5)       the network/matrix input/output format
      mcx(1)         general network/matrix tasks
      mcx diameter   compute diameter of an undirected network
      mcx ctty       compute betweenness centrality
      mcx clcf       compute clustering coefficient
      mcx erdos      compute shortest paths in graphs
      mcx query      analyse networks at different thresholds
      mcx alter      apply network transformations
      mcx convert    convert between interchange/binary storage types
      mcxarray(1)    transform array data to MCL matrices
      mcxdump(1)     dump a matrix optionally with label substitions
      mcxload(1)     load label data into matrix and tab files
      mcxrand(1)     randomly remove, add, and perturb edge weights
      mcxmap(1)      relabel indices in a graph/matrix
      mcxsubs(1)     extracting submatrices in various ways
      mcxi(1)        general matrix operations
      mcxassemble(1) create matrices from raw data
      clm(1)         general graph-clustering related tasks
      clm dist       compute split/join distance between clusterings
      clm vol        derive node volatility scores from a set of clusterings
      clm info       compute performance measure for clusterings
      clm meet       compute intersection of clusterings
      clm mate       find best matching clusters between clusterings
      clm close      fetch connected components from graphs or subgraphs
      clm imac       interpret MCL iterand/matrix as clustering
      clm  order      reorder indices to represent blocks from different clus-
                     terings
      clm residue    extend subgraph clustering
      clmformat(1)   display clusters as html or txt files
      mclpipeline(1) parsing/assembly/clustering/display
      mclblastline(1)BLAST pipeline
      mcxdeblast(1) *parse BLAST files

      Entries marked * are not available if only a default install is done.













  mcl 1.008, 09-308           4 Nov 2009                          1


