MO640 - Exercises - DNA Evolution Models, Durand-lec-notes (2014), Felsenstein (2004)- chapters 11 and 13

Exercises marked with (*) require further reading/search beyond the suggested texts.

3. Find the Jukes-Cantor and Kimura distances between the following sequences:
CTAGGCTTACGATTACGAGGATCCAAATGGCACCAATGCT
CTACGCTTACGACAACGAGGATCCGAATGGCACCATTGCT

Answer:

The distances were calculated on the R environment with the ape package (that stands for Analysis of Phylogenetics and Evolution). Its dist.dna function implements many molecular evolutionary models that are extensively described in the literature [1].

You need to have installed the R environment. If your system makes a distinction between the user version of a package and the development version (e.g., RPM and Debian/Ubuntu’s), remember that you need both versions installed. The development package usually has the same name but with the extension ‘-devel’ or ‘-dev’. You need root privileges to install new R packages in a system-wide manner, but you can also install them for your user only.

After entering the R environment, follow the recipe:

	> install.packages("ape", dependencies = TRUE)
        (various instalation steps ...)
	> library(ape)
	> a = 'CTAGGCTTACGATTACGAGGATCCAAATGGCACCAATGCT'
	> b = 'CTACGCTTACGACAACGAGGATCCGAATGGCACCATTGCT'
	> ab = rbind(
	         unlist(strsplit(a,"")),
	         unlist(strsplit(b,""))
	     )
	> bin = as.DNAbin(as.alignment(ab))
	> jukescantor = dist.dna(bin, model = "JC69")
	jukescantor
	          1
	2 0.1367412
	> kimura = dist.dna(bin, model = "K80")
	kimura
	          1
	2 0.1368157

References:
[1] R Documentation - Pairwise Distances from DNA Sequences. Accessed 2015-03-28.

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