MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Internal configuration of this server has changed on Jan 12, which should make no change in user interface.  If you notice any unexpected changes, then please let us know.

Add long sequence(s) to existing alignment  in Alpha testing (2015/Jun)

Existing alignmentExample
Gaps (-) will be preserved.

or upload a plain text file:     Clear

Long sequence(s) to be added to the above alignmentExample
Gaps (if any) will be removed.

or upload a plain text file:     Clear


UPPERCASE / lowercase:

Direction of nucleotide sequences:


Output order:

Sequence title:

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

↓ Failed when the "allow unusual symbols" option was on, Jan/18 –.  Fixed Jan/20, 2022.
Keep alignment length:

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

Positions of insertions in added sequences and in the reference alignment will be returned by the --compactmapout option. Updated (2021/Dec)


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.