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