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 default 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 of memory:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=2G   # Request 2GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load mcl

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

References

• MCL website
• MCL manual