# 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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mcxconvert(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<cat-file-in> <cat-file-out> mcx convert [--cone-to-stack]--write-binary<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--stack-to-cone,-h,--apropos,--version,-set,--nop<num> are accessible in all mcx modes. They are described in the mcx manual page. mcx convert [-progress(transform cone file to stack file)] [--cone-to-stack(transform stack file to cone file)] [--stack-to-cone(output native binary format)] [--write-binary(read and write cat format)] [--cat<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-cat-maxoption, mcx{convert} will out- put a one-line synopsis describing the matrix in the argument. The-qand--cone-to-stackoptions 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--stack-to-cone(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.--cone-to-stack(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.--stack-to-cone(read and write cat format)--cat<num> (limit the stack conversion to <num> matrices)-cat-max(output native binary format) This option is only useful with either of the options--write-binary,--cone-to-stack, or--stack-to-coneAUTHOR 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)--cat.