MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

To align a set of closely related sequences, put a reference (or, arbitrarily selected) sequence into the "Existing alignment" box, and put other sequences to the "Fragmentary sequence(s)" box.  Detailed procedure

This function may be unstable, as urgently updated to use more resources, 2020/Apr/11.  If you have any problems, please send feedback.

Updated to support ∼10,000 sequences × ∼30,000 sites, 2020/Apr/16.  Maybe unstable.  If you have any problems, please send feedback.

Reduced the frequency of "timeout" error in data transfer, 2020/Jul/27.  Upload a zipped file when data is large.

Add fragmentary sequence(s) to existing alignment or sequence Help  Help for closely-related long data

Existing alignmentExample
Gaps (-) will be preserved.

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

Fragmentary sequence(s) to be added to the above alignmentExample
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

Keep alignment length: in Alpha testing (2015/May)

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

A correspondence table between the positions in each fragmentary 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.

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.