Molecular Evolution: dN/dS Substitution Simulator

This simulator visualises molecular evolution at the level it actually happens: single-nucleotide substitutions inside codons, competing under natural selection. A gene of adjustable length is rendered as a 3D ribbon of codon triplets; each tick, random point mutations are proposed, classified as synonymous or nonsynonymous against the standard genetic code, and accepted or rejected with a probability set by your chosen selection regime (ω). Live dN, dS and dN/dS statistics — computed with the classic Nei-Gojobori site-counting method — let you watch purifying selection suppress protein change, neutral drift treat both mutation classes equally, or positive selection drive amino-acid turnover faster than silent change, the same signature biologists use to detect selection in real sequence data.