MAFFT Multiple Sequence Alignments

Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "MAFFT version 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids Research, 33 511-518

MAFFT is a program for the multiple alignment of nucleic acid or protein sequences, and is available from the Web Service→Alignment→MAFFT Multiple Sequence Alignment entry in the web services menu.

MAFFT utilizes algorithms for spectral correlation to identify homologous regions in a fast-fourier transform representation of each sequence. The Jalview web service runs MAFFT using the '--auto' option which picks optimal parameters for the set of sequences to be aligned.