text: user2841: 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?
  
  user191: 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.
  
original_text: 2841: <p>Is it possible to fit branch models <a href="https://link.springer.com/article/10.1007/PL00006320" rel="nofollow noreferrer">(Yang and Nielsen, 1998)</a> in <a href="https://bitbucket.org/Davydov/godon/src" rel="nofollow noreferrer">godon</a>? That is, the model which averages over all sites, as opposed to the branch site models?</p>
   191: <p>Branch-models are currently not implemented in godon. In the PAML manual Ziheng Yang writes:</p>
  <blockquote>
  <p>This model is very parameter-rich and its use is discouraged.</p>
  </blockquote>
  <p>This was one of the reasons I did not implement it.</p>
  <p><em>Disclaimer: I am the author of godon.</em></p>
  