WeightedLD: The Application of Sequence Weights to Linkage Disequilibrium

Sequence-weighting methods are commonly employed to account for biases in sequence datasets. We use a weighting scheme which considers the observed distinctiveness of sequences and apply it to calculations of linkage disequilibrium. Each sequence now contributes a weighted score to linkage disequilibrium measurements of pairwise loci. We demonstrate that this reduces the effect of uneven sampling, as underrepresented groups of sequences will each contribute more individually than redundant, similar sequences.