For a large number of short sequences,
try an experimental service (2016/Jul).
or upload a plain text 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.)
Direction of nucleotide sequences: Help
Same as input
Adjust direction according to the first sequence (accurate enough for most cases)
Adjust direction according to the first sequence (only for highly divergent data; extremely slow)
Same as input
Notify when finished (optional; recommended when submitting large data):
FFT-NS-1 (Very fast; recommended for >2,000 sequences; progressive method)
FFT-NS-2 (Fast; progressive method)
G-INS-1 (Slow; progressive method with an accurate guide tree)
Iterative refinement methods
FFT-NS-i (Slow; iterative refinement method)
E-INS-i (Very slow; recommended for <200 sequences with multiple conserved domains and long gaps)
L-INS-i (Very slow; recommended for <200 sequences with one conserved domain and long gaps)
G-INS-i (Very slow; recommended for <200 sequences with global homology)
(Extremely slow; secondary structure of RNA is considered; recommended for a global alignment of highly divergent ncRNAs with <200 sequences × <1,000 nucleotides; the number of iterative cycles is restricted to two, 2016/May)
This feature is available only when G-INS-1 or G-INS-i is selected in the Strategy section above.
Try to align gappy regions anyway
Leave gappy regions (Not recommended for >∼1,000 sequences)
↑ Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.
↓ Long stretches of Ns tend to be gapped (excluded from the alignment).
↑ Try this if Ns should be aligned with usual letters.