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I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short example since I just want to learn the process (we are expected to use online resources to figure out our homework problems since it is an online class, but I can't find any examples).

Human: GGATGCGCCT
Sheep: GGACGCGCCT
Chicken: GGACACGCCT

Can someone show me how to do this? Here is my guess from the limited info I found, but I have little to no confidence that it is correct:

p-distance of human/chicken = 2
p-distance of sheep/chicken = 1
relative rate of evolution = 2/1 = 2

Is this correct? If not, can someone show me how to do it correctly?

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1 Answer 1

up vote 2 down vote accepted

This kind of thing is normally calculated using the $K_{a}/K_{s}$ ratio, the ratio of synonymous to non-synonymous substitutions. It is not enough to count mutations for coding sequences, you should also take into account whether or not that mutation will actually change the resulting product.

There are various online tools that can help you do this, for example Phylemon:

http://phylemon.bioinfo.cipf.es/evolutionary.html

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