Multiple alignment program for amino acid or nucleotide sequences

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

or upload a plain text file:     Clear

New 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

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:

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

Keep alignment length: in Alpha Testing (2015/May)
Yes
Supported only when one of Progressive methods is selected in the panel below.   Not yet compatible with Auto or Iterative refinement methods.
With this option, insertions in the new sequenes are deleted, to keep the alignment length the same as the input alignment.

Positions of insertions in added sequences and in the reference alignment will be returned by the --compactmapout option. Updated (2021/Dec)

Strategy:
Auto (FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size)   Updated!  2017/Dec

Progressive methods
FFT-NS-2 (Fast)
G-INS-1 (Slow; uses all-pair global alignment)
L-INS-1 (Slow; uses all-pair local alignment)

Iterative refinement methods   New!  2017/Dec
FFT-NS-i (Slow)
G-INS-i (Slower; uses all-pair global alignment)
L-INS-i (Slower; uses all-pair local alignment)

Parameters:
Scoring matrix for amino acid sequences: BLOSUM30 BLOSUM45 BLOSUM62 BLOSUM80 JTT100 JTT200
Scoring matrix for nucleotide sequences: 1PAM / κ=2 20PAM / κ=2 200PAM / κ=2

↑ 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.