Enter your Input Sequences, choose a Scoring Matrix, and set your Gap Opening Penalty and Gap Extension Penalty to calculate the Total Alignment Score for your Multiple Sequence Alignment — toggle Normalize by Length to also get your Average Pairwise Score, Overall Identity, and Gap Percentage across all aligned sequences.
Total Alignment Score
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Average Pairwise Score
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Overall Identity
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Gap Percentage
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A multiple sequence alignment score quantifies the quality of an alignment by considering matches, mismatches, and gaps between sequences. Higher scores indicate better alignments with more conserved regions.
Gap opening penalties are applied when a gap is introduced, while gap extension penalties are applied for each position the gap continues. Higher penalties discourage gaps and favor longer continuous matches.
BLOSUM62 is recommended for protein sequences with moderate evolutionary distance. PAM250 works better for distantly related proteins. Use identity matrix for exact match scoring.
Identity percentage shows the proportion of positions where all sequences have identical residues. It's a measure of sequence conservation across the entire alignment.
Yes, normalizing by length makes scores comparable between alignments of different sizes and accounts for the tendency of longer alignments to have higher raw scores.
The average pairwise score is computed by scoring all possible sequence pairs in the alignment and taking their mean. This provides insight into overall alignment quality.
Sequences should be provided in FASTA format with sequence names preceded by '>' and aligned sequences on separate lines. Gaps should be represented with '-' characters.