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mcxalter(1) [debian man page]

mcxalter(1)							  USER COMMANDS 						       mcxalter(1)

  NAME
      mcxalter - various network transformations

  SYNOPSIS
      mcxalter [-imx <fname> (specify matrix input)] [-abc <fname> (specify label input)] [-tab <fname> (use tab file)] [-o <fname> (output)] [-tf
      spec (apply tf-spec to input matrix)]

  DESCRIPTION
      This utility supplies various transformations of networks.

  OPTIONS
      -abc <fname> (label input)
	The file name for input that is in label format.

      -imx <fname> (input matrix)
	The file name for input that is in mcl native matrix format.

      -tab <fname> (use tab file)
	This option causes the output to be printed with the labels found in the tab file.  With -abc this option will, additionally, construct  a
	graph  only on the labels found in the tab file.  If this option is used in conjunction with -imx the tab domain and the matrix domain are
	required to be identical.

      -tf <tf-spec> (transform input matrix values)
	Transform the input matrix values according to the syntax described in mcxio(5).

      -o fname (output file)
	Output file.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcxalter 12-068						      8 Mar 2012							 mcxalter(1)

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mcx ctty(1)							  USER COMMANDS 						       mcx ctty(1)

  NAME
      mcx ctty - compute betweenness centrality for network nodes

  SYNOPSIS
      mcx ctty [options] [matrix-file]

      mcxctty  is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode ctty.
      The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described  in  the  mcx  manual
      page.

      mcx  ctty  [-abc	<fname> (specify label input)] [-imx <fname> (specify matrix input)] [-extent <int> (only consider paths of length at most
      <int>)] [-o <fname> (output file name)] [-tab <fname> (use tab file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs  are
      used)]  [-j  <intj>  (this  job has index <intj>)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version,
      exit)]

  DESCRIPTION
      mcx ctty computes betweenness centrality for all nodes in a graph, using the between centrality update algorithm from [1].

      The input graph/matrix, if specified with the -imx option, has to be in mcl matrix/graph format. You can use label input	instead  by  using
      the  -abc  option.   Refer  to  mcxio(5) for a description of these two input formats.  By default mcx diameter reads from STDIN and expects
      matrix format.  To specify label input from STDIN use -abc -.

  OPTIONS
      -abc <fname> (label input)
	The file name for input that is in label format.

      -imx <fname> (input matrix)
	The file name for input. STDIN is assumed if not specified.

      -o <fname> (output file name)
	The name of the file to write output to.

      -extent <int> (only consider paths of length at most <int>)
	This option will lead to different results. Results will still be informative however, being representative for the local context in which
	nodes reside. It does probably not make sense to use values smaller than four or five.

      -tab <fname> (use tab file)
	This  option causes the output to be printed with the labels found in the tab file.  With -abc this option will, additionally, construct a
	graph only on the labels found in the tab file.  If this option is used in conjunction with -imx the tab domain and the matrix domain  are
	required to be identical.

      -t <int> (use <int> threads)
      -J <intJ> (a total of <intJ> jobs are used)
      -j <intj> (this job has index <intj>)
	Computing  centrality  scores in a graph is time-intensive.  If you have multiple CPUs available consider using as many threads. Addition-
	ally it is possible to spread the computation over multiple jobs/machines.  Conceptually, each job takes a  number  of	threads  from  the
	total  thread  pool.  If  job control is used (the -J option is used) then the number of jobs should not exceed the number of threads. The
	total number of threads divided by the total number of jobs defines the number of threads that will be used by the current job.  Addition-
	ally,  the  number  of	threads specified signifies the total added amount of all threads across all machines and must be the same for all
	jobs. This number is used by each job to infer its own set of tasks.  The following set of options, if given to as many commands,  defines
	three jobs, each running four threads.

	-t 12 -G 3 -g 0
	-t 12 -G 3 -g 1
	-t 12 -G 3 -g 2

  REFERENCES
      [1]  Ulrik  Brandes, A Faster Algorithm for Betweenness Centrality.  Journal of Mathematical Sociology 25(2): 163-177, (2001).  http://cite-
      seerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.11.2024

  SEE ALSO
      mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcx ctty 12-068						      8 Mar 2012							 mcx ctty(1)
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