Recently I have been very interested in calculating the dN/dS ratio to estimate rates of nonsynonymous and synonymous substitutions. Since I've just started learning the theory, I have a few basic questions (apologies if any of these are stupid!). Thanks for your help!
One of the applications I'm interested in is estimating selection pressure on various viral genomes. Does it make sense to use dN/dS across coding sequences from different viruses; e.g. an analysis considering HCV, HIV, and influenza all together?
relatedly, what is the best way to estimate dN/dS within species, and is there an existing implementation? I ask because of this paper, which explains why we shouldn't rely on dN/dS within species...http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000304
is it possible to use dN/dS on whole genome coding sequences within species? I obtained CDSs for 4 strains of HCV from NCBI (NC_009823, NC_009824, NC_009825, NC_009826) and ran them through FEL in data monkey (http://www.datamonkey.org/fel), but the results said that there were no regions under positive or negative selection. This seems wrong to me..so it is likely that I'm doing the analysis incorrectly.