Misorientation rateΒΆ

Based on Baudry & Depaulis (Genetics 2003 165:1619-1622), the class stats.ProbaMisoriented estimates the rate of invalid orientation of polymorphisms using an outgroup, accounting for parallel mutations in the branch leading to the outgroup. Only diallelic sites (with on maximum one additional allele in the outgroup) are considered.

The proportion of transitions among substitutions among diallelic (in the ingroup) polymorphism is denoted \(T_i\). The proportion of transversions is given by \(T_v = 1 - T_i\).

The transition rate is then \(\alpha = \frac{T_i}{4}\) and the transversion rate is \(\beta = \frac{T_v}{8}\)

The transition to transversion rate ratio is computed as:

\[\kappa = \frac{\alpha}{\beta}\]

And the probability of misorienting a site is:

\[P_M = \frac{\alpha^2 + 2 \beta^2}{2 \beta (2 \alpha + \beta)}P_D\]

where \(P_D\) is given by proportion of polymorphic sites where the outgroup has a third allele.