Multiple alignment program for amino acid or nucleotide sequences

Sub MSA a:  Example
Gaps (-) will be preserved, except for gap-only sites.

or upload a plain text file:     Clear

Sub MSA b:  Example
Gaps (-) will be preserved, except for gap-only sites.

or upload a plain text file:     Clear

Sub MSA c ...  Example

Sub MSA d ...  Example

Sub MSA e ...  Example

Orphan sequences ...  Example

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

Sequence title:
Same as input
Insert group ID (a, b, c, d, e, O) at the head of sequence title

Title length in Clustal format (only first word is used as title):
(10 – 100)

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:

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

Progressive methods
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) 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; the number of iterative cycles is restricted to two, 2016/May) Help

Align unrelated segments, too? in Alpha Testing (2014/Mar)
If the input data is expected to be globally conserved but locally contaminated by unrelated segments, try 'Unalignlevel>0' and possibly 'Leave gappy regions'.

Unalignlevel:
0.0 0.8

↑ Default
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

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 this to '1PAM / κ=2' when aligning closely related DNA sequences.

Gap opening penalty: (1.0 – 5.0)
Offset value: (0.0 – 1.0)

Score of N in nucleotide data: Example

↓ Long stretches of Ns tend to be gapped (excluded from the alignment).

(nzero) N has no effect on the alignment score.
(nwildcard) N is treated like a wildcard. Experimental option (2016/Apr/26)

↑ Try this if Ns should be aligned with usual letters.

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)