Evolutionary distance models

Question

[samuel.zachej]

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 :)

Answer 1

[ben.ward]

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, 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.

Answer 2

[Gabriel R.]

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. I looked briefly and you can request the source code and that will give you some code to work with.

[samuel.zachej]

Thanks, but I have only student access to those journals and those major papers about models from their authors are paid and it is too expensive for me :D and your link doesn't work for me, don't know why .. just 404. I will send them a request at least for equations.

Thank you. Sam

[Gabriel R.]

send me an email if you need help

[Biomonster]

The link provided by Gabriel works, except that you have to delete the ")" after the link in your address bar.

Good luck with your project!

[samuel.zachej]

Nice, thanks I will try to download the package and take a look into the code. Thank you and sorry for my late response, I had a free week so Havent been at home.