next up previous contents
Next: HKY85 model (Hasegawa-Kishino-Yano, 85) Up: Nucleotide substitution models implemented Previous: JC69 model (Jukes-Cantor, 69)   Contents

K80 model (Kimura, 80)

The Kimura model assumes equal base frequencies and accounts for the difference between transitions and transversions with one parameter. $\pi_i = \frac{1}{4} \quad \forall i, \quad
\alpha_{transition} = 1.0, \quad
\alpha_{transversion} = \alpha_1$


Table 2.2: K80 transition matrix
\begin{table}{\large\begin{displaymath}
Q = m_r \times \left(
\begin{array}{cccc...
...1 & 0.25 & 0.25\alpha_1 & * \\
\end{array}\right)
\end{displaymath}}\end{table}




Gowri-Shankar Vivek 2003-04-24