Fig. 3

Simulation. We present the simulation steps of two nucleotides pairs along a phylogenetic tree of 4 leafs. In red we highlight the nucleotide changes. (1.) We randomly pick a state at the root. (2.) We assign internal node states using the transition probability matrix P(t)=e ^Qt where Q is the Coev instantaneous rate matrix and t is the branch length [7]. (3.) The simulated pairs are the pairs assigned to the leafs of the phylogenetic tree