mcl is an implementation of the Markov Cluster Algorithm, aka MCL algoritm. It is described in the mcl manual. Several other applications are part of the MCL distribution. This manual pages gives an overview.
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mcl(1)
the cluster algorithm
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mclfaq(7)
MCL Frequently Asked Questions
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mcxio(5)
the network/matrix input/output format
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mcx(1)
general network/matrix tasks
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mcx diameter
compute diameter of an undirected network
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mcx ctty
compute betweenness centrality
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mcx clcf
compute clustering coefficient
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mcx erdos
compute shortest paths in graphs
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mcx query
analyse networks at different thresholds
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mcx alter
apply network transformations
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mcx convert
convert between interchange/binary storage types
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mcxarray(1)
transform array data to MCL matrices
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mcxdump(1)
dump a matrix optionally with label substitions
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mcxload(1)
load label data into matrix and tab files
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mcxrand(1)
randomly remove, add, and perturb edge weights
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mcxmap(1)
relabel indices in a graph/matrix
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mcxsubs(1)
extracting submatrices in various ways
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mcxi(1)
general matrix operations
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mcxassemble(1)
create matrices from raw data
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clm(1)
general graph-clustering related tasks
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clm dist
compute split/join distance between clusterings
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clm vol
derive node volatility scores from a set of clusterings
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clm info
compute performance measure for clusterings
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clm meet
compute intersection of clusterings
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clm mate
find best matching clusters between clusterings
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clm close
fetch connected components from graphs or subgraphs
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clm imac
interpret MCL iterand/matrix as clustering
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clm order
reorder indices to represent blocks from different clusterings
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clm residue
extend subgraph clustering
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clmformat(1)
display clusters as html or txt files
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mclpipeline(1)
parsing/assembly/clustering/display
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mclblastline(1) *
BLAST pipeline
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mcxdeblast(1) *
parse BLAST files
Entries marked * are not available if only a default install is done.