I have a dataset of resequenced genomes for many populations yet only with two individuals per population. I would now like to compare patterns of linkage disequilibrium (LD) across populations. I already used the correlated zygosity statistics for single genomes that was developped by Lynch et al. 2014 and for which the software mlRho exists. However, I was wondering if there is any solution to calculate more conventional estimates for LD? Neither PLINK nor VCFtools seem to be able to handle this.