Sequence Alignment Visualizer (Needleman-Wunsch)

Sequences

Sequence 1 (rows)

A / C / G / T · up to 12 letters

Sequence 2 (columns)

A / C / G / T · up to 12 letters

Scoring

Match score +1

Mismatch penalty −1

Gap penalty −2

Result

Optimal score

–

Alignment length

–

% identity

–

How it works

Needleman-Wunsch fills an (n+1)×(m+1) grid where cell (i,j) holds the best score for aligning the first i letters of sequence 1 against the first j letters of sequence 2. Each cell only needs its three neighbours — diagonal (match/mismatch), above (gap in sequence 2) and left (gap in sequence 1) — so the whole matrix can be swept row by row, exactly as the bars fill in here.

F(i,0) = i · gap        F(0,j) = j · gap
F(i,j) = max(
  F(i-1,j-1) + s(xᵢ,yⱼ),   // diagonal: match or mismatch
  F(i-1,j)   + gap,        // up: gap in sequence 2
  F(i,j-1)   + gap         // left: gap in sequence 1
)

Bar height / colour — each column's height and hue encode F(i,j); brighter cyan means a higher running score.
Traceback (yellow line) — starting at the bottom-right corner F(n,m), it walks back to whichever neighbour produced that cell's score, all the way to F(0,0). Reading the path top-left→bottom-right gives the optimal alignment.
Match / mismatch / gap — raise the match reward or soften the gap penalty to favour longer runs of aligned letters; a harsher gap penalty pushes the path toward the diagonal instead.

This exact recurrence, extended with affine gap costs and substitution matrices like BLOSUM, underlies global aligners used throughout genomics and protein analysis.

DP score (low) DP score (high) Traceback path

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Enter two sequences and press Align.

Sequence Alignment Visualizer — Needleman-Wunsch