RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This service was unavailable due to a network trouble around Jul 3.  If you don't receive result of your job, please retry.

Hardware was upgraded, Jan 16, 2022.  There should be no change in user interface.  If you notice any unexpected changes, then please let us know.

To avoid overload, try a light-weight option, for MSA of full-length SARS-CoV-2 genomes (2020/Apr). 

For a large number of short sequences, try an experimental service.

Experimental service for aligning raw reads (2019/Aug)

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:

Job name (optional; used as output file name and subject of emails):

(basic Latin alphabet, number and space only)

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.

Guide tree:


To display the tree, follow the “Refine dataset” link in the result page.

Mafft-homologs (Collects homologs by PSI-BLAST and aligns homologs with input sequences; Protein only): Help

Number of homologs: (5 – 600)

Threshold: E = (1e-1 – 1e-40)

Plot LAST hits (DNA only):