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mugsy website  

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.

Environment Modules

Run module spider mugsy to find out what environment modules are available for this application.

System Variables

  • HPC_MUGSY_DIR - installation directory


If you publish research that uses mugsy you have to cite it as follows:

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