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.
Version v1r2.3. Freely available for every user.
Initialize module with command:
module add mugsy-v1r2.3
mugsy --directory $SCRATCHDIR --prefix mygenomes xxx1.fasta xxx2.fasta xxx3.fasta
Documentation is available at http://mugsy.sourceforge.net/#started.