


  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>  (con-
      catenated 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  clus-
      ters  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 con-
      tain multiple clusterings. The output is by default written  as  a  con-
      catenation  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                          1


