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JC69 model (Jukes-Cantor, 69)

The Jukes-Cantor model assumes equal base frequencies and equal mutation rates, therefore it does not have any free parameter. $\pi_i = \frac{1}{4} \ quad \forall i, \quad \alpha_{ij} = 1.0 \quad \forall i, \forall j \neq i$

Table 2.1: JC69 transition matrix
\begin{table}{\large\begin{displaymath} Q = m_r \times \left( \begin{array}{cccc... ... T & 0.25 & 0.25 & 0.25 & * \\ \end{array}\right) \end{displaymath}}\end{table}



Gowri-Shankar Vivek 2003-04-24