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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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    $\begingroup$ 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 $\endgroup$
    – NatWH
    Feb 2 at 11:49
  • $\begingroup$ The votes to close are because your question lacks a lot of detail. $\endgroup$
    – user438383
    Feb 2 at 12:54
  • $\begingroup$ And yet, it has all of the information necessary for the question to be answered. $\endgroup$
    – NatWH
    Feb 2 at 14:53
  • $\begingroup$ Voted to open, because it's exactly the type of questions we aim for - concise, concrete and answerable. $\endgroup$
    – Kamil S Jaron
    Feb 2 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.

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