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HKY85 model (Hasegawa-Kishino-Yano, 85)

The HKY85 model does not assume equal base frequencies and accounts for the difference between transitions and transversions with one parameter. $\alpha_{transition} = 1.0, \quad
\alpha_{transversion} = \alpha_1$

Table 2.3: HKY85 transition tatrix
Q = m_r \times \left(
...& \pi_C & \pi_G\alpha_1 & * \\

Gowri-Shankar Vivek 2003-04-24