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