Getting distance matrix from specific models for AA/Nt MSA

Question

[Klios3th]

Hi,

How would I go about getting a distance matrix with specific models (GTR, WAG, HKY) for my msa? I need it for a python project. I found code for the older models like Kimura, Tamura, logdet but the newer models are somehow much harder to find.

I know that RAXML use these models for their tree phylogeny but i dont know how to extract their distance matrix?

Does anyone have any insight? Thanks in advance