Multiple Sequence Alignment (MSA) Viewer — paste 2–30 protein sequences in FASTA format. Alignment runs entirely in your browser (progressive MSA, UPGMA guide tree, BLOSUM62, gap open −11 / extend −1); no data is uploaded.

Color scheme:

Alignment

Hydrophobic AILMFWV Positive KRH Negative DE Polar NQST Cys Gly Pro Aromatic FY * fully conserved  : conserved substitution
Engine: progressive multiple alignment (UPGMA guide tree on pairwise identity, profile–profile sum-of-pairs with BLOSUM62, affine gap −11/−1), implemented in JavaScript and executed locally in your browser. For large or divergent datasets, a dedicated tool such as MAFFT/MUSCLE remains the reference standard.
⟺ Paste at least two protein sequences and click Run Alignment.
Conserved columns are marked * (identical) and : (conserved substitution);
a per-column conservation bar and the pairwise identity matrix are shown below the alignment.