RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Some jobs were canceled due to a network trouble, Jul.12.  If you don't receive result of your job, please resubmit.

This service is under maintenance for hardware replacement, Jul, 2024.  During the maintenance, the service can be unstable and size of input data is limited.

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 (Updated, 2023/Nov)

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





UPPERCASE / lowercase:

Direction of nucleotide sequences: Help

Output order:

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.


↑ Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.

(1.0 – 5.0)

(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

(5 – 600)

(1e-1 – 1e-40)

Plot LAST hits (DNA only):