MAFFT (Multiple sequence Alignment based on Fast Fourier Transform)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 <～10,000 sequences), etc.
- Windows/Mac OsX/ Linux
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Katoh, Rozewicki, Yamada 2019
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Briefings in Bioinformatics 20:1160-1166
Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees.
Yamada KD, Tomii K, Katoh K.
Bioinformatics. 2016 Jul 4. pii: btw412
Kazutaka Katoh and Hiroyuki Toh
Parallelization of the MAFFT multiple sequence alignment program
Bioinformatics (2010) 26 (15): 1899-1900