RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This service was unstable due to maintenance, 18:00 – 21:00, May 23, JST.

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)

If you need an MSA of only a specific region, then try extracting the region first (2022/Oct). New!

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:

Title length in Clustal format (only first word is used as title):

(10 – 100)

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):