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Neighbor-Joining Phylogenetics: Reconstructing Evolutionary Trees

Simulate DNA sequences evolving down a random tree, then watch the Neighbor-Joining algorithm reconstruct the evolutionary tree from pairwise sequence distances — with a live split-recovery accuracy score against the true tree.

Molecular Biology3DAdvanced60 FPS📱 Mobile-adapted

This simulator generates a random ancestral DNA sequence, evolves it down a randomly branching tree under the Jukes–Cantor substitution model, and then reconstructs the evolutionary tree from nothing but the resulting leaf sequences using the Neighbor-Joining algorithm — the same distance-based method used to build real phylogenies from sequencing data. Tune the substitution rate, sequence length and number of taxa to see how much evolutionary signal is available, compare the true generating tree against the algorithm's reconstruction in a 3D cone layout, and track a live split-recovery accuracy score, mean pairwise distance and total inferred tree length.

⚙ Under the hood

Watch a DNA sequence evolve down a random tree under the Jukes-Cantor model, then reconstruct the evolutionary tree from the resulting sequences using the Neighbor-Joining algorithm, with a live accuracy score against the true tree.

phylogeneticsneighbor-joiningDNA sequencingmolecular evolutionbioinformaticsbiotechnology

3D · Three.js / WebGL renderer · 60 FPS target · runs fully client-side, no install