Multiple Sequence Alignment

ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools.

Important notice: ClustalW2 will be retired from EMBL-EBI service in August 2015. We recommend users migrate to Clustal Omega in particular for protein alignments. Other MSA tools exist for progressive alignments and may be more suitable for DNA alignments, for example MAFFT. For more help please conctact us via the feedback link above.

STEP 1 - Enter your input sequences

a set of sequences in any supported format:

Or, a file:

STEP 2 - Set your Pairwise Alignment Options
Slow Fast
STEP 3 - Set your Multiple Sequence Alignment Options
STEP 4 - Submit your job
(Tick this box if you want to be notified by email when the results are available)
If available, the title will be included in the subject of the notification email and can be used as a way to identify your analysis

If you plan to use these services during a course please contact us.

Please read the FAQ before seeking help from our support staff.