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.

**mcl(1)** the cluster algorithm

**mclfaq(7)** MCL Frequently Asked Questions

**mcxio(5)** the network/matrix input/output format

**mcx(1)** general network/matrix tasks

**mcx diameter** compute diameter of an undirected network

**mcx ctty** compute betweenness centrality

**mcx clcf** compute clustering coefficient

**mcx erdos** compute shortest paths in graphs

**mcx query** analyse networks at different thresholds

**mcx alter** apply network transformations

**mcx convert** convert between interchange/binary storage types

**mcxarray(1)** transform array data to MCL matrices

**mcxdump(1)** dump a matrix optionally with label substitions

**mcxload(1)** load label data into matrix and tab files

**mcxrand(1)** randomly remove, add, and perturb edge weights

**mcxmap(1)** relabel indices in a graph/matrix

**mcxsubs(1)** extracting submatrices in various ways

**mcxi(1)** general matrix operations

**mcxassemble(1)** create matrices from raw data

**clm(1)** general graph-clustering related tasks

**clm dist** compute split/join distance between clusterings

**clm vol** derive node volatility scores from a set of clusterings

**clm info** compute performance measure for clusterings

**clm meet** compute intersection of clusterings

**clm mate** find best matching clusters between clusterings

**clm close** fetch connected components from graphs or subgraphs

**clm imac** interpret MCL iterand/matrix as clustering

**clm order** reorder indices to represent blocks from different
clusterings

**clm residue** extend subgraph clustering

**clmformat(1)** display clusters as html or txt files

**mclpipeline(1)** parsing/assembly/clustering/display

**mclblastline(1)** * BLAST pipeline

**mcxdeblast(1)** * parse BLAST files

Entries marked * are not available if only a default install is done.