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

For more information, consult mclfamily(7).

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

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

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

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