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MCL

Markov Cluster Algorithm (MCL) is a fast and scalable unsupervised cluster algorithm for graphs based on simulation of (stochastic) flow in graphs.

MCL is available as a module on Apocrita.

Usage

To run the latest installed version of MCL, simply load the mcl module:

$ module load mcl
$ mcl
[mcl] usage: mcl <-|file name> [options], do 'mcl -h' or 'man mcl' for help

For usage documentation, run mcl --help.

Example job

Serial job

Here is an example job running on 1 core and 2GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load mcl

mcxload -abc file.abc -o seq.mci
mcl seq.mci

References