MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This page may be unstable because urgently updated to use more resouces, 2020/Apr/11.  If you have any problems, please send feedback.

To align a set of closely related sequences, put a reference (if not available, arbitrarily selected) sequence into the "Existing alignment" box, and put other sequences to the "Fragmentary sequence(s)" box.

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

Keep alignment length:

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

A correspondence table between the positions in each new sequence and the positions in the alignment will also be returned.


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.