🧬 Molecular Clock & Phylogenetic Tree Simulator (2D)

This 2D companion drives the same Poisson-substitution molecular-clock model as the 3D version — expected substitutions per branch λ = r·L·m, Jukes-Cantor correction to recover true genetic distance from observed difference, and a clock-estimated divergence time compared against the true root age — but renders it as a plain rectangular dendrogram: time runs left to right along the x-axis, species tips are stacked vertically on the right, branch colour (blue→red) encodes how much divergence each branch accumulated, and small orange dots mark individual substitution events along each branch. Switching between a strict clock (every branch the same rate) and a relaxed clock (each branch scaled by an independent random multiplier) makes visible, in the stats panel, exactly how much a relaxed clock's rate heterogeneity biases the age a molecular clock would infer from the tree alone.