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)
Check Out this Related 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)