MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Jul.12 – 13: Unstable due to maintenance.

Jul.14: If you notice any troubles after this maintenance, let us know.

For a large number of short sequences, try an experimental service (2017/Jul)  Updated

Multiple sequence alignment and NJ / UPGMA phylogeny

Paste protein or DNA sequences in fasta format.  Example

or upload a plain text file:


UPPERCASE / lowercase:

Direction of nucleotide sequences: Help


Output order:

Notify when finished (optional; recommended when submitting large data):
Email address:

Advanced settings


Progressive methods

Iterative refinement methods

Help  Updated (2015/Jun)

Align unrelated segments, too? in Alpha Testing (2014/Mar)
If the input data is expected to be globally conserved but locally contaminated by unrelated segments, try 'Unalignlevel>0' and possibly 'Leave gappy regions'.

fs0.0 fs0.8

↑ Default
This feature is available only when G-INS-1 or G-INS-i is selected in the Strategy section above.

Scoring matrix for amino acid sequences:
Scoring matrix for nucleotide sequences:
↑ Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.
Gap opening penalty: (1.0 - 5.0)
Offset value: (0.0 - 1.0)

Score of N in nucleotide data: Example
↓ Long stretches of Ns tend to be gapped (excluded from the alignment).

Experimental option (2016/Apr/26)
↑ Try this if Ns should be aligned with usual letters.

Mafft-homologs (Collects homologs from SwissProt by BLAST and performs profile-based alignments; Protein only): Help

Number of homologs: (5 - 200)
Threshold: E = (1e-5 - 1e-40)

Plot LAST hits (DNA only):