Calculate pairwise identity and similarity percentages for aligned protein sequences.
Paste aligned sequences (FASTA or GDE format). Alignment must contain at least two sequences.
Comma-separated amino acid groups used for similarity (leave empty when comparing DNA).
Paste aligned sequences in FASTA or GDE format. Ensure sequences are already aligned with gaps (marked by dashes or dots) at corresponding positions. Minimum two sequences required.
For protein alignments, enter comma-separated amino acid groups to define similarity (e.g., "GAVLI, FYW" for hydrophobic groups). Leave empty for DNA comparisons.
Click execute to calculate identity and similarity percentages for all pairwise combinations. The tool compares each sequence to every other sequence.
Results show alignment length, identical residues, similar residues (based on groups), and percent identity/similarity for each sequence pair.
Each pair of aligned sequences is compared residue by residue. Identical residues (excluding gap characters) contribute to identity, while residues appearing in the same user-defined similarity group contribute to similarity.
Percentages are reported relative to the alignment length after gap adjustments. Clear the similarity groups when analysing nucleotide alignments to report identity only.