Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

How to run Mugsy

[gqd693@login-0-0 ~]$ module load mugsy
You now need to source the $mugsyenv. Either type '. $mugsyenv' in your terminal, or add 'source $mugsyenv' to your script.
[gqd693@login-0-0 ~]$ . $mugsyenv

A sample submit script for Grid Engine

#$ /bin/bash
#$ -cwd
#$ -N mugsy_job
. /etc/profile.d/
module load mugsy
. $mugsyenv
mugsy --directory /work/abc123 --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta

-- AdminUser - 30 Mar 2017
Topic revision: r1 - 30 Mar 2017, AdminUser
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