Adding feature - customization of nucleotide substitution model in YN98 class

[Keren Halabi]

Hi dear team,

Currently, the YN98  class which is used in most site models in Bio++ uses the K80 model to model nucleotide substitutions. I was wondering if a feature could be added in the form of a parameter given to its constructor based on which the nucleotide model would be decided. This would allow to create a wider variety of codon models. I can implement this feature, if you agree.

Many thanks!

Keren

[Laurent Guéguen]

Hi Keren,

this is already possible, through the class   CodonDistanceFrequenciesSubstitutionModel.

This codon model is similar to YN98 model, but can take any nucl model, and even 3 different

nucl models, one per position.

In bppml, it is called like:

model=CodonDistFreq(model=JC69(), frequencies=F3X4())

Beware that if the nucleotide model has a non-uniform equilibrium distribution,

there will be indentifiability issues with the parameterized frequencies.

Cheers,

Laurent

[Keren Halabi]

Thank you, Laurent!

This is exactly what I needed.

Cheers,

Keren