CLUSTAL-OMEGA · MSA ENGINE

Multiple Sequence
Alignment with ClustalΩ

Align protein or nucleotide sequences from FASTA, UniProt, PDB, or file upload

1 Sequence Input choose one method ▾

Paste MultiFASTA sequences

Minimum 2 sequences required. Standard UniProt/NCBI headers are auto-detected.

UniProt Accession IDs

Sequences will be fetched from uniprot.org/{id}.fasta. Up to 50 IDs.

PDB Entry IDs

Sequences fetched from rcsb.org/fasta/entry/{id}. All chains are included.

Upload FASTA file

📂

Drop .fasta / .fa / .faa here
or click to browse

Accepts standard FASTA format. Both protein and nucleotide sequences are supported.

2 Alignment Options clustal-omega parameters ▾

Output Format

Format of the multiple alignment output.

Sequence Type

Iterations

Number of combined guide-tree/HMM iterations.

Output Tree

Generate a guide tree alongside the alignment.

Wrap output (60 cols)

Include consensus row

Residue numbering

▶ Advanced options

Max HMM Iterations

Clustering Method

Threads

Extra CLI Arguments

Raw flags passed directly to clustalo. Use with caution.