Hi,

I am trying to compare few models for evoultionary distance calculation. I want to compare just those basic ones - Jukes-Cantor, K2P, Tamura, Tamura-Nei, HKY(Hasegawa-Kishino-Yano), GTR (general time reversible = Tavare) and Falsenstein81. I have already found equations for evolutionary distance calculations for first 4 models mentioned above. I am still looking for HKY,GTR,F81. Can you help me? I mean I know how to calculate substitution rates (for transitions and transversions) but please help me how to calculate evolutionary distance then?

Thanks Sam :)
I would first look at the original papers for the different models, you will find the equations for sure. I know that the APE/phangorm package uses those but I think they merely call [phyml][1]. I looked briefly and you can request the source code and that will give you some code to work with.

 [1]: http://www.atgc-montpellier.fr/phyml