If all I have is NGS and a few isolates, is there any way to calculate recombination rate? Based on allele frequencies?
Have you tried LDHAT?
I know it is able to do it, I am however interested in the theory behind it. What does r^2 actually mean? I know it's association of different genotype frequencies, but what does it mean when it is very high or very low in terms of recombination?
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