ClustalW2 was the long-standing tool for multiple sequence alignment (MSA) of DNA or protein sequences. EMBL-EBI has retired the old ClustalW2 service in favour of Clustal Omega, which is faster and more accurate for large alignments.
Run Clustal Omega at EMBL-EBI ↗
What multiple sequence alignment is for
An MSA lines up three or more sequences to reveal conserved residues, motifs and evolutionary relationships — the basis for phylogenetics, primer design across homologs, and identifying functional sites.
Current alignment tools
- Clustal Omega — the modern successor to ClustalW2 at EBI.
- MUSCLE and MAFFT — other widely used aligners.
- MEGA — alignment plus phylogenetics in a desktop app.
Frequently asked questions
Is ClustalW2 still available?
EBI has retired the standalone ClustalW2 web service; use Clustal Omega, MUSCLE or MAFFT instead.
ClustalW2 or Clustal Omega?
Clustal Omega — it scales to far larger alignments and is the current EBI recommendation.
