MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

The hardware has been updated, 2016/Jan/5. 

The service may be unstable for a while.  If you notice any features that do not work, please send a problem report.

  • A problem in handling small nucleotide data has been fixed, 2016/Jan/6.
  • When non-ascii characters appear in sequence titles, no result was returned.  This problem has been fixed, 2016/Jan/6.
  • Fixed a mistake in strategy name (FFT-NS-2, etc) displayed in result page, 2016/Jan/7.
  • Several problems in tree estimation have been fixed, 2016/Jan/7.
  • Fixed a problem that FASTA files were displayed as HTML on Internet Explorer, 2016/Jan/12.
  • Fixed a problem that notification emails were blocked in a few cases, 2016/Jan/18.
  • Connection was unstable when the network speed was slow.  Probably fixed, 2016/Jan/25.
  • Unstable due to maintenance, Feb/8 (mon), JST.

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:


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 'Leave gappy regions'. 


↑ 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 - 3.0)
Offset value: (0.0 - 1.0)

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):