# MCL user manuals

### Installation index 09-308, 1.008

### Generic stuff

mcl - the mcl manual page | html | ps
mclfaq - the mcl FAQ | html | ps
mcxio - the mcl matrix format specification | html | ps
mclpipeline - generic pipeline (parsing/matrix creation/clustering/display) | html | ps
mcx - interface to basic matrix operations | html | ps
mcxassemble - prepare input matrix from cooccurrence scores | html | ps
mcxdump - dump matrices, optionally map indices to labels | html | ps
mcxarray - transform array data to MCL matrices | html | ps
mcxconvert - convert between ascii/binary storage types | html | ps

### Dealing with clustering results

clmformat - display clusterings in browsable format | html | ps
clmdist - compute distances between clusterings | html | ps
clminfo - performance measures for clusterings | html | ps
clmmeet - compute intersection of clusterings | html | ps
clmmate - compute best matches between two clusterings | html | ps
clmimac - Interpret Matrices (c.q. MCL iterands) As Clusterings | html | ps
clmresidue - extend subgraph clusterings onto encompassing graph | html | ps
clmorder - reorder indices to represent blocks from different clusterings | html | ps
clmclose - fetch connected components from graphs or subgraphs | html | ps

### Dealing with matrices

mcxio - the mcl matrix format specification | html | ps
mcx - interface to basic matrix operations | html | ps
mcxsubs - extract submatrices by specifiying sets of nodes and clusters | html | ps
mcxmap - remap matrix indices / relabel graph nodes | html | ps
mcxassemble - prepare input matrix from cooccurrence scores | html | ps

### Application specific parsers and wrappers

BLAST package - Documentation only available if installed with --enable-blast
mclblastline - pipeline for clustering from blast files | html | ps
mcxdeblast - prepare input from blast files | html | ps