Mafft

From Vd

Contents 1 MAFFT 1.1 Other programs and main advantages 1.2 Input 1.3 Output 1.4 What next? 1.5 Homepage 1.6 Remote desktop version download 1.7 Contact person 1.8 Citation

MAFFT

MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences.

Other programs and main advantages

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.

Input

It accepts input files in FASTA format, and automatically recognizes whether an input sequence is protein or DNA

Output

Output files are in FASTA format.

What next?

Once you have acquired an alignment you may use this multiple tasks, e.g. primer design (if nucleotide alignment), SNP detection, intron/exon border detection and phylogenetic analysis.

Homepage

http://align.bmr.kyushu-u.ac.jp/mafft/online/server/

Remote desktop version download

http://align.bmr.kyushu-u.ac.jp/mafft/software/

Contact person

Kazutaka Katoh: katoh@biophys.kyoto-u.ac.jp

Citation

Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)

Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)