I am trying to estimate the effective population size of my samples. I've seen publications that use the population recombination rate (rho) to then estimate Ne. I've been trying to use LDhat software, trying first to run the example files that come in package, but when I tried to use the pairwise program to estimate rho, I got an error message:
npt and total do not agree: not exhaustive: please use lkgen program to generate a complete lookup table for sample size
..now exiting to system...
Has anyone used this software?
Any help would be appreciated.