Multiple alignment program for amino acid or nucleotide sequences

Reference:  Example
Gaps (-) will be preserved.

or upload a plain text file:     Clear
Zipped file is acceptable.

New sequence(s) to be added to the reference above:  Example
Gaps (if any) will be removed.

or upload a plain text file:     Clear
Zipped file is acceptable.

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

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

Job name (optional):
(basic Latin alphabet, number and space only)

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

Add full-length genomes of SARS-CoV-2 to MSAs by GISAID EpiCoV:

MSA unmasked (reference=WIV04) MSA full0822 MSA full0627 MSA full0608 MSA full0523 MSA full0517 MSA codon0813 MSA codon0630 MSA codon0606 MSA codon0519 MSA codon0516

By this switch,

• Uses the reference data corresponding to the MSA selected above.
• Sets the same flags (--compactmapout, --maxambiguous and --addtotop) as the calculation in GISAID. 

Just input your new sequences to the New sequence(s) box. 

The resulting alignment can be concatenated to the entire or a part of GISAID's MSA to incorporate your new sequences into the MSA.  The GISAID MSA has to be downloaded separately from the original site.

Insert gaps at codon boundaries as possible.  Works only with GISAID's references.

--addtotop: Use only the top sequence as reference.

Ambiguous letters:
Remove sequences that have ambiguous letters more than: 0% (Use unambiguous sequences only) 1% 5% 50% 100% (Use all sequences)

and replace succesive ns (nucleotide) or Xs (protein) in new sequences with a single n or X.

Keep alignment length:
Yes
With this option, insertions at the new sequenes are deleted, to keep the alignment length the same as the input alignment.

--compactmapout: Output the positions of insertions in added sequences and in the reference alignment. Updated (2021/Dec)

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

Strategy:
Auto (--multipair or --6merpair; depends on data size)

--6merpair (Fast)
--multipair --weighti 0 (Intermediate)
--multipair (Accurate)

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.