Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size).

FFT-NS-1 (Very fast; recommended for more than 2,000 sequences; progressive method).

FFT-NS-2 (Fast; progressive method).

FFT-NS-i (Slow; iterative refinement method).

E-INS-i (Very slow; recommended for less than 200 sequences with multiple conserved domains and long gaps).

L-INS-i (Very slow; recommended for less than 200 sequences with one conserved domain and long gaps).

G-INS-i (Very slow; recommended for less than 200 sequences with global homology).

Q-INS-i (Extremely slow; secondary structure of RNA is considered; recommended for a global alignment of highly diverged ncRNAs with less than 200 sequences × less than 1,000 nucleotides).

http://mafft.cbrc.jp/alignment/server/index.html