Question: How to calculate base pair conservation for two species?
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gravatar for notsway
5.2 years ago by
notsway0
United States
notsway0 wrote:

Hi,

I'm trying to represent pair-wise conservation in the mitochondrial genome across a number of species. I want to create a diagram that looks like this. In the lower-right corner, there is a note that explains how conservation has been illustrated. I'd like to calculate average conservation for the genome and a given window. 

I'd like to know how to get a conservation score for every base, given the sequences of two species. Is there an alternative for PhyloP or PhastCons which seem to require MSA?

ADD COMMENTlink written 5.2 years ago by notsway0
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