Dear all

I have a genotype data for SNP in cattle, I calculated r^2 by plink and now I want to calculated effective population size of my population. the explanation for how calculate Ne by LD result are not clear in literature, I thinks that I have to use this formula: Ne = (1/4c)*([1/r^2] - 1 ) , The age of Ne for any distance is estimated by 1/2c. is there any one that can offer me some paper or explain clearly how i should calculated Ne from this formula. I know that I can calculate recombination rate by phase or assume that 1cM=1Mbp, and also I know that I should use r2 but I don't know if I calculated r2 in bin distance how can I chose r2 for each cM?

thanks a lot

Any luck using LDNe? I have the same problem myself, I am using genome-wide SNP data and I am not sure if that program can handle such big datasets.