RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This service will be unstable (again) while replacing a part of hardware, Jun 22 – 23. 
Alignments calculated before the replacement will be inaccessbible. 

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):