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TN93 model (Tamura-Nei, 93)

The TN93 model has four frequencies parameters. It accounts for the difference between transitions and transversions and differentiates the two kinds of transitions (purine $\leftrightarrow$purine & pyrimidine $\leftrightarrow$pyrimidine). $\alpha_{AG} = \alpha_{GA} = 1.0, \quad
\alpha_{transversion} = \alpha_1, \quad
\alpha_{CT} = \alpha_{TC} = \alpha_2$

Table 2.4: TN93 transition matrix
Q = m_r \times \left(
...alpha_2 & \pi_G\alpha_1 & * \\

Gowri-Shankar Vivek 2003-04-24