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mclfamily(7) [debian man page]

mcl(7)								  MISCELLANEOUS 							    mcl(7)

  NAME
      mclfamily - a description of the mcl family of cluster applications.

      mcl  is an implementation of the Markov Cluster Algorithm, aka MCL algoritm.  It is described in the mcl manual.	Several other applications
      are part of the MCL distribution. This manual pages gives an overview.

  DESCRIPTION
      mcl(1)	     the cluster algorithm
      mclfaq(7)      MCL Frequently Asked Questions
      mcxio(5)	     the network/matrix input/output format
      mcx(1)	     general network/matrix tasks
      mcx diameter   compute diameter of an undirected network
      mcx ctty	     compute betweenness centrality
      mcx clcf	     compute clustering coefficient
      mcx erdos      compute shortest paths in graphs
      mcx query      analyse networks at different thresholds
      mcx alter      apply network transformations
      mcx convert    convert between interchange/binary storage types
      mcxarray(1)    transform array data to MCL matrices
      mcxdump(1)     dump a matrix optionally with label substitions
      mcxload(1)     load label data into matrix and tab files
      mcxrand(1)     randomly remove, add, and perturb edge weights
      mcxmap(1)      relabel indices in a graph/matrix
      mcxsubs(1)     extracting submatrices in various ways
      mcxi(1)	     general matrix operations
      mcxassemble(1) create matrices from raw data
      clm(1)	     general graph-clustering related tasks
      clm dist	     compute split/join distance between clusterings
      clm vol	     derive node volatility scores from a set of clusterings
      clm info	     compute performance measure for clusterings
      clm meet	     compute intersection of clusterings
      clm mate	     find best matching clusters between clusterings
      clm close      fetch connected components from graphs or subgraphs
      clm imac	     interpret MCL iterand/matrix as clustering
      clm order      reorder indices to represent blocks from different clusterings
      clm residue    extend subgraph clustering
      clmformat(1)   display clusters as html or txt files
      mclpipeline(1) parsing/assembly/clustering/display
      mclblastline(1)BLAST pipeline
      mcxdeblast(1) *parse BLAST files

      Entries marked * are not available if only a default install is done.

  mcl 12-068							      8 Mar 2012							      mcl(7)

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mcx convert(1)							  USER COMMANDS 						    mcx convert(1)

  NAME
      mcx convert - convert between mcx storage types

  SYNOPSIS
      mcx convert <matrix-file-in> <matrix-file-out>
      mcx convert [--write-binary] --cone-to-stack <cat-file-in> <cat-file-out>
      mcx convert [--write-binary] --stack-to-cone <cat-file-in> <cat-file-out>

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

      mcx  convert  [--cone-to-stack  (transform  cone	file to stack file)] [--stack-to-cone (transform stack file to cone file)] [--write-binary
      (output native binary format)] [--cat (read and write cat format)] [-cat-max <num> (limit the stack conversion to <num> matrices)]

      In the two-argument invocation without additional arguments, mcx convert converts from the format found in the first file to the other  for-
      mat, i.e.  from native interchange to native binary format or the other way around. When querying with the -q option, mcx{convert} will out-
      put a one-line synopsis describing the matrix in the argument. The --cone-to-stack and --stack-to-cone options convert between the two types
      of concatenated output provided by mclcm.

  DESCRIPTION
      The  mcl	libraries make extensive use of matrices. Matrices are used to encode graphs, matrices and clusterings.  They can be stored either
      in interchange or in binary format. The latter is somewhat more efficient in storage and much faster in both reading and	writing,  but  the
      default is interchange format.

      The  mcl input routines recognize the type of storage they are dealing with. If you want to convert a matrix to the other storage type, sim-
      ply specify the file name of the matrix you want to convert.  mcx convert will recognize its type, and write the	other  type  to  the  file
      specified as the second argument.

  OPTIONS
      --cone-to-stack (transform cone file to stack file)
	This option requires two trailing options, the names of respectively the source cone file and the target stack file.

      --stack-to-cone (transform stack file to cone file)
	This option requires two trailing options, the names of respectively the source stack file and the target cone file.

      --cat (read and write cat format)

      -cat-max <num> (limit the stack conversion to <num> matrices)

      --write-binary (output native binary format)
	This option is only useful with either of the options --cone-to-stack, --stack-to-cone, or --cat.

  AUTHOR
      Stijn van Dongen.

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

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