16 May 2014
**mcl**
14-137

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.

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.