Clustal Omega

Multiple sequence alignment tool by EMBL-EBI. The standard for aligning protein or DNA sequences across species.

What It Does

• Multiple sequence alignment (MSA) of protein or DNA sequences
• Supports hundreds of sequences
• Output formats: FASTA, ClustalW, Phylip
• Generates guide trees showing evolutionary relationships

How to Use

Web

1. Go to https://www.ebi.ac.uk/jdispatcher/msa/clustalo
2. Paste sequences in FASTA format
3. Submit and view alignment

API

# Submit job
curl -X POST "https://www.ebi.ac.uk/Tools/services/rest/clustalo/run" \
  -d "email=your@email.com&sequence=>human\nMVLSPA...\n>mouse\nMVLSPA..."

Command Line

# Install
conda install -c bioconda clustalo
 
# Run alignment
clustalo -i strc_orthologs.fasta -o strc_aligned.fasta --outfmt=fasta

Verified Status

VERIFIED — used for STRC 9-species conservation analysis. E1659 position is 100% conserved (Glu) across all 9 mammals spanning ~80 million years of evolution.

STRC Research Usage

• STRC Cross-Species Conservation Analysis — aligned 9 mammalian STRC sequences
• Conservation at E1659: 100% conserved Glu across human, mouse, rat, dog, cow, pig, horse, rabbit, bat

Connections

• UniProt [depends-on] — source of ortholog sequences
• OrthoDB [see-also] — ortholog identification
• STRC Cross-Species Conservation Analysis [used-in]
• UCSC Genome Browser [see-also] — conservation track visualization