RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

To extract a short region (<5000 bases) from a set of long unaligned sequences, try another function (2022/Oct).

Options specifically for SARS-CoV-2  2022/Mar

By this switch,

  • Uses the reference data corresponding to the MSA selected above.
  • Sets the same flags (--compactmapout, --maxambiguous and --addtotop) as the calculation in GISAID. 
Just input your new sequences to the New sequence(s) box. 

The resulting alignment can be concatenated to the entire or a part of GISAID's MSA to incorporate your new sequences into the MSA.  The GISAID MSA has to be downloaded separately from the original site.

Add new sequence(s) to reference Help

Gaps (-) will be preserved.

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

New sequence(s) to be added to the reference aboveExample
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:

Title length in Clustal format (only first word is used as title):
(10 – 100)

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 new 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.