clmorder(1) [debian man page]

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  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 sec-
      ond batch covers the level-one second largest cluster, and so on. Within these constraints, each batch of second-level clusters (correspond-
      ing 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 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 12-068						      8 Mar 2012							clm order(1)

clm imac(1)							  USER COMMANDS 						       clm imac(1)

  NAME
      clm imac - Interpret Matrices (c.q. MCL iterands output by mcl) As Clusterings.

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

  SYNOPSIS
      clm imac -imx <fname> [options]

      clm imac -imx fname (input file) [-o fname (name/stem for output)] [-dag fname (output  DAG)]  [-overlap	str  (overlap  mode)]  [-sort  str
      (size|revsize|lex|none)]	[-strict  num (in 0..1)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version,
      exit)]

  DESCRIPTION
      Use clm imac to interpret matrices (as clusterings) output by mcl using mcl's -dump ite option.

      Use clm imac only if you have a special reason; the normal usage of mcl is to do multiple runs for varying -I parameters and use	the  clus-
      terings output by mcl itself.  One reason is if you are interested in clusterings with overlap; early MCL iterands generally induce cluster-
      ings possessing overlap.	Another reason is to investigate how the cluster structure associated with the MCL process evolves over time.

  OPTIONS
      -imx fname (input file)
	The input file is presumably an MCL iterand resulting from the mcl option -dump ite.

      -strict num (in 0..1)
	Higher values (up until 1) will thin out the DAG constructed by clm imac. The default value is 0.00001, yielding the full DAG.

      -o fname (file name/stem)
	Write to file named fname.

      -dag fname (output DAG)
	Write the DAG (directed acyclic graph) constructed from the input to file. This DAG is constructed according to the  structure	associated
	with  diagonally positive semi-definite matrices as described in the PhD thesis Graph clustering by flow simulation.  Consult mclfamily(7)
	for references.

      -sort str (size|revsize|lex|none)
	Sort the clusters either by increasing size, decreasing size, lexicographically by the indices they contain, or use the clustering exactly
	as obtained from the interpretation routine.

      -overlap mode (overlap mode)
	With  mode  set  to  cut,  remove  any overlap by allocating the nodes in overlap to the first cluster in which they were found. Mode keep
	leaves overlap unchanged, and mode split results in overlapping parts excised and introduced as clusters in their own right.

  AUTHOR
      Stijn van Dongen.

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

  clm imac 12-068						      8 Mar 2012							 clm imac(1)