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