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clm(1) [debian man page]

clm(1)								  USER COMMANDS 							    clm(1)

  NAME
      clm - perform various computations on graphs and clusterings

  SYNOPSIS
	 clm <mode> [mode-options] [mode-files]

  DESCRIPTION
      clm implements a variety of computations on graphs and clusterings. The first argument to clm should be a mode, which is a string establish-
      ing the type of computation to invoke. Each mode mode is described in the clmmode manual page. The currently available modes are	clm  dist,
      clm info, clm meet, clm mate, clm close, clm order, clm imac, clm vol, and clm residue.  The dist mode is thus described in the clmdist man-
      ual page.

      Invoking clm without arguments causes it to print out a list of available modes with a  short  description  of  the  type  of  command  line
      expected by that mode.

      Invoking	clm  with just a mode will print out a longer listing of options available for that particular mode.  Modes that are able to func-
      tion normally without arguments can be invoked by adding the --nop argument.

      Several options are shared between all clm modes. Note that these options are specified after the mode. See OPTIONS.

      The --version option causes clm to print out version and license information.

      Issuing clm help mode will cause clm to look for a manual page describing mode and display it if found. This requires that the MANPATH envi-
      ronment  variable  contains the directory in which the MCL-edge manual pages were installed. This will usually be PREFIX/share, where PREFIX
      is the path with which the software was configured.

  OPTIONS
      These are options that pertain to all modes. They should be specified after the mode argument.

      -h (synopsis)
      --help (synopsis)
	List available options.

      --nop (no-op)
	Not an option. This option has no effect then to increment the argument count. This can be useful for clm modes which are able to function
	without  any  options.	Such  a mode typically reads from STDIN, writes to STDOUT, and uses default settings. However, simply specifying a
	mode without options leads clm to output a list of available options for that mode. This can be averted by using the --nop option.

      -set key=val (set key-value pair)
	Sets the key key to value val in the environment.  Some modes allow adjustment of settings in this manner.

      -debug <int> (set debug level/flags)
      --debug (turn default debugging on)
      --test (turn default testing on)
	The first two turn on debugging, the last is for testing. The effect of these options is otherwise undocumented.

      --progress (enable progress reporting)
	This will enable some kind of progress reporting, by writing to STDERR.

  AUTHOR
      Stijn van Dongen.

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

  clm 12-068							      8 Mar 2012							      clm(1)

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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)
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