RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

BUG!! This feature was affected by a bug, from Mar/5 to Mar/10, 2018.

Merge two or more sub MSAs into a single MSA In alpha testing (2015/Jun) Help

Two or more sub MSAs are merged into a single MSA.  Sub MSAs are assumed to be phylogenetically separated from each other.  If it cannot be assumed, try --add or --addfragments.

Sub MSA aExample
Gaps (-) will be preserved, except for gap-only sites.

or upload a plain text file:     Clear

Sub MSA bExample
Gaps (-) will be preserved, except for gap-only sites.

or upload a plain text file:     Clear

Sub MSA c ... 

Sub MSA d ... 

Sub MSA e ... 

Orphan sequences ... 


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


Progressive methods

Iterative refinement methods


Align unrelated segments, too? in Alpha Testing (2014/Mar)
If the input data is expected to be globally conserved but locally contaminated by unrelated segments, try 'Unalignlevel>0' and possibly 'Leave gappy regions'.


↑ Default
This feature is available only when G-INS-1 or G-INS-i is selected in the Strategy section above.

Scoring matrix for amino acid sequences:
Scoring matrix for nucleotide sequences:
↑ Switch this to '1PAM / κ=2' when aligning closely related DNA sequences.
Gap opening penalty: (1.0 – 5.0)
Offset value: (0.0 – 1.0)

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.

Plot LAST hits (DNA only):