mclindex(7) MISCELLANEOUS mclindex(7)
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 specifiying 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
mclindex 12-068 8 Mar 2012 mclindex(7)