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 :)
R packages such as APE and Phangorn and so on allow you to compute evolutionary distance measures. Both packages and other related, phylogenetic based packages are written - at least in part - by the same author: Paradis.

The function dist.dna, for example, accepts as input an aligned set of DNA sequences, and has an optional parameter "model", which allows you to choose from many different evolutionary models, including all the ones you are looking to use here. http://www.inside-r.org/packages/cran/ape/docs/dist.dna. If you'd like to see how that function implements various models you could take a look at the code - although some of it is likely written in C as well as R.

If you read a book like the Phylogenetic Handbook [here][1], where they discuss the mathematical derivations of distance measures - in fact there is a chapter dedicated to it - you will learn the classic models are in fact specific cases of the GTR model.

 [1]: http://www.cambridge.org/gb/academic/subjects/life-sciences/genomics-bioinformatics-and-systems-biology/phylogenetic-handbook-practical-approach-phylogenetic-analysis-and-hypothesis-testing-2nd-edition