Input Sequences
Minimum 2 sequences. Set Protein / DNA / RNA in Alignment Options.
Find IDs at uniprot.org —
the short code at the top of each entry (e.g. P69905).
Sequences are fetched automatically. Always protein.
Find IDs at rcsb.org —
the 4-character code at the top of each entry (e.g. 1HHO).
Chain suffixes stripped automatically (e.g. 1SBIA → 1SBI). Always protein.
Drop FASTA file here or click to browse
.fasta .fa .fas .txt .seq · max 16 MB
Alignment Options
⚠ UniProt and PDB always return protein sequences. Sequence type locked to Protein.
Additional flags passed directly to clustalo. Use with care.
Run Alignment
ClustalOmega performs progressive multiple sequence alignment using HMM profile techniques.
Supports protein, DNA, and RNA sequences.
Alignment Results
Submit sequences to run alignment