Is it possible to fit branch models (Yang and Nielsen, 1998) in godon? That is, the model which averages over all sites, as opposed to the branch site models?
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1$\begingroup$ For those VTCing this - Bioinformatics.SE is the specified help forum for the godon package. If you've got a problem, take it up with the meta $\endgroup$– NatWHCommented Feb 2, 2021 at 11:49
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$\begingroup$ The votes to close are because your question lacks a lot of detail. $\endgroup$– user438383Commented Feb 2, 2021 at 12:54
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$\begingroup$ And yet, it has all of the information necessary for the question to be answered. $\endgroup$– NatWHCommented Feb 2, 2021 at 14:53
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$\begingroup$ Voted to open, because it's exactly the type of questions we aim for - concise, concrete and answerable. $\endgroup$– Kamil S JaronCommented Feb 2, 2021 at 21:52
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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.
answered Feb 2, 2021 at 12:50