The MCL family
Keywords: manual

16 May 2014 mcl 14-137

1.
NAME
2.
DESCRIPTION

## 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

mcl

the cluster algorithm

mclfaq

MCL Frequently Asked Questions

mcxio

the network/matrix input/output format

mcx

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

transform array data to MCL matrices

mcxdump

dump a matrix optionally with label substitions

mcxload

load label data into matrix and tab files

mcxrand

randomly remove, add, and perturb edge weights

mcxmap

relabel indices in a graph/matrix

mcxsubs

extracting submatrices in various ways

mcxi

general matrix operations

mcxassemble

create matrices from raw data

clm

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

display clusters as html or txt files

mclpipeline

parsing/assembly/clustering/display

mclblastline `*`

BLAST pipeline

mcxdeblast `*`

parse BLAST files

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