MAFFT

Multiple Alignment through Fast Fourier Transform is available here.

References

1. Katoh K, Kuma K, Toh H, and Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33(2):511-8. DOI:10.1093/nar/gki198 |
2. Katoh K, Misawa K, Kuma K, and Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002 Jul 15;30(14):3059-66.