LDNE: a program for estimating effective population size from data on linkage disequilibrium

LDNE is a program with a Visual Basic interface that implements a recently developed bias correction for estimates of effective population size (N-e) based on linkage disequilibrium data. The program reads genotypic data in standard formats and can accommodate an arbitrary number of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. LDNE calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use.