MAFFT 

MAFFT (multiple sequence alignment based on the fast Fourier transform (FFT)) is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i wich is accurate for alignment with less than 200 sequences, FFT-NS-2 which is fast for alignment with less than 10000 sequences. MAFFT includes two novel techniques. (i) Homologous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. (http://mafft.cbrc.jp/alignment/software/ )