The Clustal family of programs performs multiple sequence alignment (MSA) of DNA, RNA or protein sequences. The current version is Clustal Omega, which replaced the older ClustalW/ClustalW2.
Run Clustal Omega at EMBL-EBI ↗
Clustal Omega vs ClustalW
Clustal Omega uses a faster, more scalable algorithm (HMM-based, seeded guide trees) that aligns thousands of sequences accurately — a big improvement over the older ClustalW2 for large datasets. For small alignments both give good results.
How to run an alignment
- Paste your sequences in FASTA at Clustal Omega.
- Choose DNA or protein and submit.
- Review the alignment and the guide tree; export for downstream phylogenetics (e.g. in MEGA).
Frequently asked questions
What is the current Clustal program?
Clustal Omega, available at EMBL-EBI; it replaced ClustalW and ClustalW2.
What is Clustal used for?
Aligning multiple DNA/RNA/protein sequences to find conserved regions and build the basis for phylogenetic analysis.
