mclindex(7)

NAME
mclindex - a list of the utilities and modules present in the MCL distribution. For more information, consult mclfamily(7).

Generic stuff
the mcl manual page
the mcl FAQ
the mcl matrix format specification
generic pipeline (parsing/matrix creation/clustering/display)
interface to basic matrix operations
prepare input matrix from cooccurrence scores
dump matrices, optionally map indices to labels
transform array data to MCL matrices
convert between ascii/binary storage types

Dealing with clustering results
display clusterings in browsable format
compute distances between clusterings
performance measures for clusterings
compute intersection of clusterings
compute best matches between two clusterings
Interpret Matrices (c.q. MCL iterands) As Clusterings
extend subgraph clusterings onto encompassing graph
reorder indices to represent blocks from different clusterings
fetch connected components from graphs or subgraphs

Dealing with matrices
the mcl matrix format specification
interface to basic matrix operations
extract submatrices by specifiying sets of nodes and clusters
remap matrix indices / relabel graph nodes
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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pipeline for clustering from blast files
prepare input from blast files