Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-02T12:50:37.607Z
Answers.LastActivityDate: 2021-02-02T12:50:37.607Z
Answers.UserDisplayName: Iakov Davydov
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-02T11:49:19.880Z
Comments.Text: 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](https://bioinformatics.meta.stackexchange.com/questions/240/im-a-bioinfo-software-developer-and-i-would-like-to-use-bioinformatics-se-as-t)
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-02T12:54:02.580Z
Comments.Text: The votes to close are because your question lacks a lot of detail.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-02T14:53:46.253Z
Comments.Text: And yet, it has all of the information necessary for the question to be answered.
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-02T21:52:38.137Z
Comments.Text: Voted to open, because it's exactly the type of questions we aim for - concise, concrete and answerable.
Comments.UserDisplayName: Kamil S Jaron
Tags: <phylogenetics><codon><godon>
Title: Fitting branch models with godon
ThreadText: # Fitting branch models with godon
  
  (Asked by: username_0 on 2021-01-29)
  
  Is it possible to fit branch models [(Yang and Nielsen, 1998)](https://link.springer.com/article/10.1007/PL00006320) in [godon](https://bitbucket.org/username_3/godon/src)? That is, the model which averages over all sites, as opposed to the branch site models?
  
  **Tags:** phylogenetics, codon, godon
  
  > **Comments:**
  > **username_0**: 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](https://bioinformatics.meta.stackexchange.com/questions/240/im-a-bioinfo-software-developer-and-i-would-like-to-use-bioinformatics-se-as-t)  
  > **username_1**: The votes to close are because your question lacks a lot of detail.  
  > **username_0**: And yet, it has all of the information necessary for the question to be answered.  
  > **username_2**: Voted to open, because it's exactly the type of questions we aim for - concise, concrete and answerable.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2021-02-02. Score: 2 | Accepted answer
  
  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.*
  
  
  ---
  
  