Documentation

A probability matrix, P_ij(t) = Pr (X_t = j | X_0 = i).

Make type signatures a little clearer.

The important matrix that gives the probabilities to move from one state to another in a specific time (branch length).

Move from a given state to a new one according to a transition probability matrix .

This function is the bottleneck of the simulator and takes up most of the computation time.