Trees -- Simulation studies and tree topologies by ms()

The R script (ex_trees.r) uses ms() to generate trees based on Coalescent Theory in different conditions and scenarios and draws in the following plot. Each panel has 50 samples in 3 groups (15, 20, 15). In the plot, the conditions, $(r_a, r_d, h_s)$, indicate the growth rate of ancestral trees, the growth rate of descendent trees, and the total height of the trees, respectively. The scenarios, max, equal and star are different scaling methods for descendent trees. These trees can be applied to seqgen() to generate sequences for simulation and bootstrap studies.