Clustal-Omega — Multiple Sequence Alignment

Step 1 — Input sequences

Paste FASTA sequences (starting with ">"), a list of UniProt accessions (e.g. P69905 Q8I6R7), or a list of PDB IDs (e.g. 1HHO 4HHB).
The format is detected automatically — no selector needed.

Sequences or IDs * Min. 2 sequences required. Max recommended: 500 sequences / 100k residues. Please provide at least 2 sequences.

Upload a FASTA file (.fasta / .fa / .txt). The file will be sent directly to Clustal-Omega. Maximum upload size is determined by server PHP settings.

FASTA file Accepted formats: .fasta, .fa, .txt

Step 2 — Output & options

Output format * Clustal (.aln) is the standard human-readable format.

Sequence type

Additional options

--dealign (remove existing gaps before alignment)

How it works

# Input is detected automatically:
#  - Starts with '>'           → FASTA (used directly)
#  - 6–10 char accessions      → UniProt: fetch https://www.uniprot.org/uniprot/{id}.fasta
#  - 4 char alphanumeric IDs   → PDB:     fetch https://www.rcsb.org/fasta/entry/{id}
#  - File upload               → FASTA file (passed directly)

# Clustal-Omega is then called:
clustalo -i input.fasta -o output.clu --outfmt=clustal --force
  