getPij of class AbstractSubstitutionModel

[Keren Halabi]

Hi dear team,

There is something that is not entirely clear to me.

In the documentation of the class AbstractSubstitutionModel, I see: "...The freq_ vector and generator_ matrices are hence the only things to provide to create a substitution model." However, I see that in many of the implemented models in Bio++, the function getPij implementation that is available in AbstractSubstitutionModel - which is a class that they inherit from indirectly or directly (for example, class HKY85 which inherits from the previous indirectly via AbstractReversibleNucleotideSubstitutionModel) - is not used in practice (that is, there is an implementation of the function in the respective class to be used instead).

I was wondering why that is, and if using the implementation of the function in AbstractSubstitutionModel should yield the desired transition probabilities, provided that the generator_ and freq_ are set properly.

Many thanks!

Keren

[Laurent Guéguen]

Hi Keren,

in some nucleotide models, the computation of the transition probabilities is analytical,

so there is no need to use all the computation defined in AbstractSubstiittuionModel.

Cheers,

Laurent

[Keren Halabi]

Hi Laurent,

Sorry for the delay and thank you for the clarification!

Cheers,

Keren