I have several population samples, and was able to align my illumina reads to a reference genome and call variants.
I am interested to test whether the organism is asexual, and that would involve testing for LD. Since I don't have phased data, I used plink to calculate r^2 using dprime. It is an approach described here "http://www.biomedcentral.com/1471-2105/8/428" and uses MLE to estimate haplotype frequency.
Can someone help me understand how this approach tests for recombination? If in one sample you have 2 biallelic markers at frequency X and in the second sample you have the same frequency X for the same 2 bi allelic markers, that means that for those 2 SNPs no recombination is happening? Why would recombination change allele frequencies?