MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Not efficient for full-length MSA of closely-related viral genomes.
Try "addfragments" option for closely-related sequences.

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

Add new sequence(s) to an existing alignment  Help 

Existing alignmentExample
Gaps (-) will be preserved.

or upload a plain text file:     Clear

New 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: in Alpha Testing (2015/May)

Supported only when one of Progressive methods is selected in the panel below.   Not yet compatible with Auto or Iterative refinement methods.
With this option, insertions in 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)


Progressive methods

Iterative refinement methods   New!  2017/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.