For more information, consult mclfamily(7).
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mcl(1)
the mcl manual page
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mclfaq(7)
the mcl FAQ
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mcxio(5)
the mcl matrix format specification
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mclpipeline(1)
generic pipeline (parsing/matrix creation/clustering/display)
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mcx(1)
interface to basic matrix operations
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mcxassemble(1)
prepare input matrix from cooccurrence scores
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mcxdump(1)
dump matrices, optionally map indices to labels
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mcxarray(1)
transform array data to MCL matrices
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mcxconvert(1)
convert between ascii/binary storage types
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clmformat(1)
display clusterings in browsable format
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clmdist(1)
compute distances between clusterings
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clminfo(1)
performance measures for clusterings
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clmmeet(1)
compute intersection of clusterings
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clmmate(1)
compute best matches between two clusterings
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clmimac(1)
Interpret Matrices (c.q. MCL iterands) As Clusterings
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clmresidue(1)
extend subgraph clusterings onto encompassing graph
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clmorder(1)
reorder indices to represent blocks from different clusterings
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clmclose(1)
fetch connected components from graphs or subgraphs
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mcxio(5)
the mcl matrix format specification
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mcx(1)
interface to basic matrix operations
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mcxsubs(1)
extract submatrices by specifiying sets of nodes and clusters
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mcxmap(1)
remap matrix indices / relabel graph nodes
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mcxassemble(1)
prepare input matrix from cooccurrence scores
BLAST package - Documentation only available if installed with --enable-blast
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mclblastline(1)
pipeline for clustering from blast files
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mcxdeblast(1)
prepare input from blast files