RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

For SARS-CoV-2, use this version (2022/May).

Use 1/2 threads only (temporary option, 2021/Jan)

As of Nov 2020, a small number of strange SARS-CoV-2 genome sequences, LR897977.1‐LR898047.1, are in public databases.  Some of these sequences have one-base deletions at every ∼60 bases seemingly because of a computational error, which can cause problems in alignment calculation requiring more RAM.  For smooth calculation,

  • Remove these sequences.
  • If these sequences are necessary for your analysis, include them and turn on this switch to save memory usage.

Add fragmentary sequence(s) to existing alignment or sequence Help 

Existing alignmentExample1 (protein)
Gaps (-) will be preserved.

or upload a plain text file:     Clear
Zipped file is acceptable.

Fragmentary sequence(s) to be added to the above alignmentExample1 (protein)
Gaps (if any) will be removed.

or upload a plain text file:     Clear
Zipped file is acceptable.


UPPERCASE / lowercase:

Direction of nucleotide sequences:


Output order:

Sequence title:

Job name (optional):
(basic Latin alphabet, number and space only)

Notify when finished (optional; recommended when submitting large data):
Email address:

Advanced settings

Ambiguous letters:
and replace succesive ns (nucleotide) or Xs (protein) in new sequences with a single n or X.

Keep alignment length:

With this option, insertions at the fragmentary sequenes are deleted, to keep the alignment length the same as the input alignment.

↑ Failed when the "allow unusual symbols" option was on, Jan/18 –.  Fixed Jan/20, 2022.


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)
↑ If long gaps are not expected, set it as 0.1 or larger value.

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.