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.
module spider mugsy to find out what environment modules are available for this application.
- HPC_MUGSY_DIR - installation directory
If you publish research that uses mugsy you have to cite it as follows: