Clustal Omega
Multiple Sequence Alignment Tool
Alignment Parameters
Alignment Title (Optional)
Input Sequences or IDs to align
Auto-detect enabled:
You may paste raw FASTA sequences, PDB IDs, or UniProt IDs. The system will automatically detect the format
Important: You must enter exactly ONE identifier per line. Do not use spaces or commas.
Or Upload a FASTA File
File upload will override the text box above.
Output Format
Clustal
FASTA
MSF
Phylip
Selex
Stockholm
Vienna
Advanced Algorithm Options (Optional)
HMM Refinement Iterations:
0 (Fastest, Default)
1
2
3 (Maximum accuracy)
Dealign Input:
Remove existing gaps from sequences before aligning
Full Distance Matrix:
Slower calculation, but highly accurate for small datasets
Reset
Execute Alignment