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Satsuma is a whole-genome synteny aligner based on the Fast Fourier Transform and a battleship-style search. Parallelization is built-in.
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.
For more information, documentation and recent activity, please check out our project web page: http://satsuma.sourceforge.net/
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