RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Hardware was upgraded, Jan 16, 2022.  There should be no change in user interface.  If you notice any unexpected changes, then please let us know.

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.

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

Sequences with more than 5% ambiguous letters are removed by default.  The threshold can be changed in the Remove uninformative sequeces panel below.  2020/Oct

Updated to support more than 20,000 sequences × ∼30,000 sites, 2021/Jan.  Maybe unstable.  If you have any problems, please send feedback.

Improved the speed when Keep alignment length option is on, 2021/Jan/26. 

The upper limit of input file size is currently 4GB or 2GB, depending on browser.  If you need to input a larger file, then compress the file before uploading.  zip and gzip are acceptable, 2021/Jan/28.

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  Help for closely-related long data

Existing alignmentExample1 (protein) Example2 (SARS-CoV-2)
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) Example2 (SARS-CoV-2)
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

Remove uninformative sequences: New! (2020/Oct)
Remove sequences that have ambiguous letters more than:

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.