Multiple alignment program for amino acid or nucleotide sequences

Input:
Paste protein or DNA sequences in fasta format.  Example

or upload a file:

Use structural alignment(s)

Structural alignment 1 (optional):
Paste an alignment in fasta format.  Example
These sequences will be aligned with the 'input' sequences above, being used as a constraint.

 
Structural alignment 2 (optional):

 
Structural alignment 3 (optional):

 
Structural alignment 4 (optional):


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; extremely slow)  Beta

Output order:
Same as input
Aligned

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

Strategy:
Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size)

FFT-NS-1 (Very fast; recommended for >2,000 sequences; progressive method)
FFT-NS-2 (Fast; progressive method)
(Medium; iterative refinement method, two cycles only)
FFT-NS-i (Slow; iterative refinement method)
E-INS-i (Very slow; recommended for <200 sequences with multiple conserved domains and long gaps) Help
L-INS-i (Very slow; recommended for <200 sequences with one conserved domain and long gaps) Help
G-INS-i (Very slow; recommended for <200 sequences with global homology) Help
Q-INS-i (Extremely slow; secondary structure of RNA is considered; recommended for a global alignment of highly divergent ncRNAs with <200 sequences × <1,000 nucleotides) Help

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.

Mafft-homologs (Collects homologs from SwissProt by BLAST and performs profile-based alignments; Protein only): Help
On
Show homologs (if any)
Number of homologs: (5 - 200)
Threshold: E = (1e-5 - 1e-40)

Plot LAST hits (DNA only):
The top sequence vs the others The longest sequence vs the others
Plot and alignment Plot only Alignment only
Threshold: score=39 (E=8.4e-11) score=22 (E=0.00805) score=20 (E=0.0699) score=12 (E=398)