Man pages sections > man7 > mclindex


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
 
__________________
 
 

mclblastline(1)
 
pipeline for clustering from blast files
 

mcxdeblast(1)
 
prepare input from blast files
16 May 2014 mclindex 14-137