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MAFFT v6.864 is a multiple alignment program for amino acid or nucleotide sequences.
The original website for this application is

Paste your sequences in the FASTA format into the window :

File Pasted

Data (amino acids) example in the FASTA format


Email address (optional field; the results will be also sent to you by email)

Strategy (See MAFFT algorithms)
Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size)
FFT-NS-2 (Fast; progressive method)
FFT-NS-1 (Very fast; recommended for >2000 sequences; progressive method with a rough guide tree)
FFT-NS-i (Medium; iterative refinement method, two cycles only)
FFT-NS-i (Slow; iterative refinement method)
E-INS-i (Very slow; recommended for <200 sequences with multiple conserved domains and long gaps)
L-INS-i (Very slow; recommended for <200 sequences with one conserved domain and long gaps)
G-INS-i (Very slow; recommended for <200 sequences with global homology)
Manual parameters (see below)

Manual parameters (See MAFFT manual)
Tree rebuilding number (default=2)
Maxiterate (default=0)
Perform FFTS
Do not use FFT approximation (for long aligment)

Other parameters
Sequence type (nucleotides or amino acids)
Output format
Output order
Substitution matrix (Amino acids)
Substitution matrix (Nucleotides) * Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.
Gap opening penalty (1.0 - 3.0)
Offset penalty (0.0 - 1.0) *If long gaps are not expected, set it as 0.1 or larger value.

Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005 Jan 20;33(2):511-8. (doi: 10.1093/nar/gki198)

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Boc, A., Diallo, Alpha B. and Makarenkov, V. (2012), T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks, Nucleic Acids Research, 40(W1), W573-W579.

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