RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

For SARS-CoV-2, use this version (2022/May).

Add fragmentary sequence(s) to existing alignment or sequence Help 

Existing alignmentExample1 (protein)
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)
Gaps (if any) will be removed.

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

Help

UPPERCASE / lowercase:

Direction of nucleotide sequences:

  Beta
  Beta

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

Ambiguous letters:
and replace succesive ns (nucleotide) or Xs (protein) in new sequences with a single n or X.

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.

Strategy:



Parameters:
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.