MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
Katoh, K. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), 3059–3066. http://doi.org/10.1093/nar/gkf436
Katoh, K., Kuma, K., Toh, H., & Miyata, T. (2005). MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33(2), 511–8. http://doi.org/10.1093/nar/gki198
Katoh, K., & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9(4), 286–98. http://doi.org/10.1093/bib/bbn013
Katoh, K., Asimenos, G., & Toh, H. (2009). Multiple alignment of DNA sequences with MAFFT. In Bioinformatics for DNA sequence analysis (pp. 39–64). Springer.
Katoh, K., & Frith, M. C. (2012). Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics (Oxford, England), 28(23), 3144–6. http://doi.org/10.1093/bioinformatics/bts578
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–80. http://doi.org/10.1093/molbev/mst010
