How similar are two genes? Type two DNA sequences and watch dynamic programming find their optimal alignment, gaps and all — the bedrock algorithm of bioinformatics.
Sequence Alignment (Needleman-Wunsch)Live
global DNA alignment
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The Needleman-Wunsch algorithm finds the optimal global alignment of two sequences by dynamic programming, filling a scoring matrix and tracing back the best path. It is the foundation of bioinformatics — comparing genes, proteins, and genomes. The heatmap shows the accumulated score matrix.
Reading this result: Low similarity: only 0% of columns match (score 0). The optimal alignment leans on -2-penalty gaps and mismatches, so the sequences share little common structure.
Runs locally in your browser — free forever. Scale to the cloud when reality gets heavy.
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How it works
Needleman-Wunsch computes the best global alignment of two sequences by filling a scoring matrix with match, mismatch, and gap penalties, then tracing back the highest-scoring path. It guarantees the optimal alignment and underlies tools for comparing genes, proteins, and whole genomes. The heatmap shows the accumulated score matrix and the panel shows the aligned sequences.
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The math, the assumptions, real-world uses, or a code translation — explained for this exact simulation.
Is this Needleman-Wunsch sequence alignment tool really free?▾
Yes. Sequence Alignment (Needleman-Wunsch) runs entirely in your browser using your device's own compute, so local use is free forever. You only pay Compute Tokens if you scale a job to the cloud.
Do I need to install anything?▾
No. Everything runs client-side in a modern browser — no downloads, no license, no account required to start.
Can I save or share my simulation?▾
Create a free account to save projects, and use a shareable embed or minted DOI to publish a live, interactive version anywhere.
How accurate are the results?▾
The solver uses established numerical methods, but results are for research and educational purposes and should be validated against experiment or professional review before you rely on them.