# What are the p01sum and p0prop parameters in godon?

When using branch-site model in Godon, model optimization results include the following parameters: p01sum and p0prop. What are those and how do they relate to p0 and p1 in the branch-site model?

Disclaimer: I'm the author of godon. The question above comes from the real communication with a software user.

In the godon implementation of the branch-site model I performed the following reparametrization:

$$p_{01sum} = p_0 + p_1$$

$$p_{0prop} = \frac{p_0}{p_0 + p_1}$$.

• Both parameters have a well defined range $$(0, 1)$$.
• There is less dependency between the two. E.g., $$p_2=1-p_0-p_1$$ (proportion of sites under positivie selection) does not depend on $$p_{0prop}$$.
• Both properties are very helpful for both likelihood maximization and MCMC.

In case you are interested in $$p_0$$ and $$p_1$$ there is a straightforward way to go back to the original parameters:

$$p_0=p_{0prop}*p_{01sum}$$

$$p_1=p_{01sum}-p_0$$.

P.S. I also added this information to the tutorial.

• Damn, I totally missed this package. Godon is seriously nice, great work! Jun 3, 2020 at 13:23