ClustalW Alignments

ClustalW is a program for multiple sequence alignment. It works with both DNA and protein sequences, and can also perform profile profile alignments to align two or more multiple sequence alignments.

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice.
Nucleic Acids Research 22 4673-4680

There are two versions of this alignment function, which will operate on the selected region, if any, or the whole sequence set:

• Web Service→Alignment→ClustalW Multiple Sequence Alignment
  Aligns using the clustalW program, ignoring any gaps in the submitted sequence set.
• Web Service→Alignment→ClustalW Mulitple Sequence Alignment Realign
  Submits the sequences with existing gaps to clustalW, which will preserve existing gaps and re-align those regions which are not optimal.