Multiple alignment program for amino acid or nucleotide sequences

Existing alignment:  Example
This alignment will be preserved.

or upload a file:

New sequence(s) to be added to the above alignment:  Example
If an alignment is given here, the gaps will be removed and then a new alignment will be built.

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  Experimental!!
Adjust direction according to the first sequence (for highly diverged data; very slow)  Experimental!!

Output order:
Same as input
Aligned

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

Strategy:
Auto (FFT-NS-1 or L-INS-i; depends on data size)

FFT-NS-1 (Fast)
G-INS-1 (Slow; uses all-pair global alignment)
L-INS-1 (Slow; 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 - 3.0)
Offset value: (0.0 - 1.0)

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