Mugsy is a multiple whole genome alignment tool.


Mugsy generates a MAF (multiple alignment format) file containing the multiple alignments from FASTA inputs.

This implementation runs with two files only: reference vs contigs/draft(s). For multiple alignment a single Multi-FASTA file containing all contigs should be provided.


Mugsy: Fast multiple alignment of closely related whole genomes.
S.V. Angiuoli and S.L. Salzberg.
Bioinformatics (2011), 27 (3): 334-342.