MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

BUG!! When the "Output order: Aligned" switch is set and remote homologs are added, the order of sequences was confusing.  This problem has been fixed 2015/Jul.  In the fixed version, remote homologs are placed at the end of the output.

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:

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.