MAFFT is the multiple alignments using Fast Fourier transform. It is high speed multiple sequence alignment program.

Because it offers a range of multiple alignment methods. It can align > 1000,000 bp and > 10,000 sequences.

The most commonly used alignment strategies have their own command aliases. Part of them is listed below.
1. L-INS-i(probably most accurate ; recommended for <200 sequences; iterative alignments method incorporating local pair wise alignment information)
2. G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pair wise alignment information)
3. E-INS-i (suitable for sequences containing large unalienable regions; recommended for <200 sequences)
4. Alignment of two alignments

It can align the nucleotide base pairs and protein sequences.
Amino acids converted to numerical values based on polarity and volume.
Nucleotides converted to four -dimensional vectors based on frequencies of A, C, T, G.