What it does

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.

License and citation

This Galaxy tool is Copyright © 2012-2014 CRS4 Srl. and is released under the MIT license.

You can use this tool only if you agree to the license terms of: Mugsy.

If you use this tool, please cite:

• Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics 30(13), 1928-1929
• Angiuoli, S. V., Salzberg S. L. (2010) Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 27(3), 334-342.