<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>

CC BY-SA 4.0
2021-02-02T12:50:37.607Z
2021-02-02T12:50:37.607Z
Iakov Davydov
<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>

CC BY-SA 4.0
2021-02-02T11:49:19.880Z
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)
NatWH
CC BY-SA 4.0
2021-02-02T12:54:02.580Z
The votes to close are because your question lacks a lot of detail.
user438383
CC BY-SA 4.0
2021-02-02T14:53:46.253Z
And yet, it has all of the information necessary for the question to be answered.
NatWH
CC BY-SA 4.0
2021-02-02T21:52:38.137Z
Voted to open, because it's exactly the type of questions we aim for - concise, concrete and answerable.
Kamil S Jaron
<phylogenetics><codon><godon>
Fitting branch models with godon
# 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/Davydov/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.  

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## 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.*


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