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Branch-models are currently not implemented in godon. In the PAML manual Ziheng Yang writes: This model is very parameter-rich and its use is discouraged. This was one of the reasons I did not implement it. Disclaimer: I am the author of godon.


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Ah wait you mentioned a branch sites test, right that makes sense. You've got two or more identical sequences in the analysis. Ensure there are no identical sequences in your alignments and ... PRESTO! It will work :-) Below are my original thoughts before I re-read your question. I've kept the notes because it helps explain the theory a bit. There is no ...


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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: $p_{01sum} = p_0 + p_1$ $p_{0prop} = \frac{p_0}{p_0 + p_1}$. This has the following advantages: Both parameters have a well defined range $(0, 1)$...


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