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
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)