mcl(7)

NAME
mclfamily - a description of the mcl family of cluster applications. 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.

DESCRIPTION
the cluster algorithm
MCL Frequently Asked Questions
the network/matrix input/output format
general network/matrix tasks
compute diameter of an undirected network
compute betweenness centrality
compute clustering coefficient
compute shortest paths in graphs
analyse networks at different thresholds
apply network transformations
convert between interchange/binary storage types
transform array data to MCL matrices
dump a matrix optionally with label substitions
load label data into matrix and tab files
randomly remove, add, and perturb edge weights
relabel indices in a graph/matrix
extracting submatrices in various ways
general matrix operations
create matrices from raw data
general graph-clustering related tasks
compute split/join distance between clusterings
derive node volatility scores from a set of clusterings
compute performance measure for clusterings
compute intersection of clusterings
find best matching clusters between clusterings
fetch connected components from graphs or subgraphs
interpret MCL iterand/matrix as clustering
reorder indices to represent blocks from different clusterings
extend subgraph clustering
display clusters as html or txt files
parsing/assembly/clustering/display
BLAST pipeline
parse BLAST files
Entries marked * are not available if only a default install is done.