Add new sequences to an existing alignment using MAFFT

To extract a short region (<5000 bases/amino acids) from a set of long unaligned sequences, try another function (2022/Oct).

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

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

Existing alignment: Example1 (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 alignment: Example1 (protein)
Gaps (if any) will be removed.

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

Allow unusual symbols (Selenocysteine "U", Inosine "i", non-alphabetical characters, etc.) Help

UPPERCASE / lowercase:
Same as input
Amino acid → UPPERCASE / Nucleotide → lowercase

Direction of nucleotide sequences:
Same as input
Adjust direction according to the first sequence (accurate enough for most cases) Beta
Adjust direction according to the first sequence (only for highly divergent data; very slow) Beta

Output order:
Same as input
Aligned

Sequence title:
Same as input
Insert "New|" at the head of title of each new sequence

Title length in Clustal format (only first word is used as title):
(10 – 100)

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:
Remove sequences that have ambiguous letters more than:

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

Keep alignment length:
Yes
With this option, insertions at the fragmentary sequenes are deleted, to keep the alignment length the same as the input alignment.

--compactmapout: Output the positions of insertions in added sequences and in the reference alignment. Updated (2021/Dec)

↑ Failed when the "allow unusual symbols" option was on, Jan/18 –. Fixed Jan/20, 2022.

Strategy:
Auto (--multipair or --6merpair; depends on data size)

--6merpair (Fast)
--multipair --weighti 0 (Intermediate)
--multipair (Accurate)

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).

(nzero) N has no effect on the alignment score.

(nwildcard) N is treated like a wildcard. Experimental option (2016/Apr/26)

↑ Try this if Ns should be aligned with usual letters.

Multiple alignment program for amino acid or nucleotide sequences

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

Advanced settings