Add new sequences to an existing alignment using MAFFT

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 fragmentary sequence(s) to existing alignment or sequence Help

Existing alignment: Example
Gaps (-) will be preserved.

or upload a plain text file: Clear

Fragmentary sequence(s) to be added to the above alignment: Example
Gaps (if any) will be removed.

or upload a plain text file: Clear

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

Notify when finished (optional; recommended when submitting large data):
Email address:

Advanced settings

Keep alignment length: in Alpha testing (2015/May)
Yes
With this option, insertions at the fragmentary sequenes are deleted, to keep the alignment length the same as the input alignment.

A correspondence table between the positions in each fragmentary sequence and the positions in the alignment will also be returned.

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 - 3.0)
Offset value: (0.0 - 1.0)

↑ If long gaps are not expected, set it as 0.1 or larger value.

Multiple alignment program for amino acid or nucleotide sequences

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

Advanced settings