Nucleotide substitution matrix

As default, we use a $\kappa = 3$ Kimura (1980) nucleotide matrix, i.e.

$$\mathbf{Q} = \left[ \begin{array}{rrrr} -1.0 & 0.6 & 0.2 & 0... ... & -1.0 & 0.6 \\ 0.2 & 0.2 & 0.6 & -1.0\\ \end{array} \right],$$ (6)

where the row and column order is U, C, A, G. This corresponds to equal equilibrium nucleotide frequencies $\pi_j$ and a transition:transversion ratio of $\kappa = 3$.