NAME¶

mclindex - a list of the utilities and modules present in the MCL distribution.

For more information, consult mclfamily(7).

Generic stuff¶

mcl(1)
the mcl manual page


mclfaq(7)
the mcl FAQ


mcxio(5)
the mcl matrix format specification


mclpipeline(1)
generic pipeline (parsing/matrix creation/clustering/display)


mcx(1)
interface to basic matrix operations


mcxassemble(1)
prepare input matrix from cooccurrence scores


mcxdump(1)
dump matrices, optionally map indices to labels


mcxarray(1)
transform array data to MCL matrices


mcxconvert(1)
convert between ascii/binary storage types

Dealing with clustering results¶

clmformat(1)
display clusterings in browsable format


clmdist(1)
compute distances between clusterings


clminfo(1)
performance measures for clusterings


clmmeet(1)
compute intersection of clusterings


clmmate(1)
compute best matches between two clusterings


clmimac(1)
Interpret Matrices (c.q. MCL iterands) As Clusterings


clmresidue(1)
extend subgraph clusterings onto encompassing graph


clmorder(1)
reorder indices to represent blocks from different clusterings


clmclose(1)
fetch connected components from graphs or subgraphs

Dealing with matrices¶

mcxio(5)
the mcl matrix format specification


mcx(1)
interface to basic matrix operations


mcxsubs(1)
extract submatrices by specifying sets of nodes and clusters


mcxmap(1)
remap matrix indices / relabel graph nodes


mcxassemble(1)
prepare input matrix from cooccurrence scores

Application specific parsers and wrappers¶

BLAST package - Documentation only available if installed with --enable-blast
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mclblastline(1)
pipeline for clustering from blast files


mcxdeblast(1)
prepare input from blast files