clm order(1)                    USER COMMANDS                     clm order(1)



  NAME
      clm order - reorder clusterings conformal to inclusion structure

      clmorder is not in actual fact a program. This manual page documents the
      behaviour and options of the clm program when invoked in mode order. The
      options -h, --apropos, --version, -set, --nop are accessible in all clm
      modes. They are described in the clm manual page.

  SYNOPSIS
      clm order [-prefix <string> (file multiplex prefix)] [-o <fname>
      (concatenated output in single file)] <cluster|stack>+

  DESCRIPTION
      Given a set of input clusterings clm order first transform it into a
      stack of strictly nesting clusterings. It does this by splitting
      clusters where necessary.  It then reorders the coarsest (i.e. level-
      one) clustering, from large to small clusters. After that it reorders
      the second coarsest clustering conformally such that the first batch
      among its reordered clusters covers the level-one largest cluster, the
      second batch covers the level-one second largest cluster, and so on.
      Within these constraints, each batch of second-level clusters
      (corresponding to a single first-level cluster) is again ordered from
      larger to smaller clusters. This process is applied recursively
      throughout the entire stack of input clusters.

      The input can be specified in multiple files, and a single file may
      contain multiple clusterings. The output is by default written as a
      concatenation of matrix files, the so-called stack format. Use the -o
      option to specify the output file. The stacked format can be converted
      to Newick format using mcxdump(1). The output can be written to multiple
      files, one for each projected clustering, by using the -prefix option.
      By example, -prefix P leads to output in files named P1, P2, ..PN, where
      N is the number of clusters in the input, P1 is the most fine-grained
      ordered clustering, and PN is the coarsest clustering.

  OPTIONS
      -prefix (<string>)
      -o (<fname>)
        As decribed above.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mclfamily(7) for an overview of all the documentation and the utilities
      in the mcl family.



  clm order 1.008, 09-308           4 Nov 2009                      clm order(1)
