ClustalW version 2 (ClustalW2) is a general purpose multiple sequence alignment (MSA) program for DNA or protein sequences. This classic MSA tool uses a tree-based progressive alignment strategy to align multiple sequences in a reasonable time.

For RNA or protein sequence alignments, or larger alignments with hundreds of sequences it is suggested that Clustal Omega is used instead of ClustalW2, due to improved accuracy and performance for these types of alignment.