EMIBD9: Estimating 9 condensed IBD coefficients, inbreeding and relatedness from marker genotypes.

EMIBD9 is a computer programme implementing two likelihood methods for estimating the 9 condensed IBD coefficients, Δ = {Δ, Δ, …, Δ}, between a pair of individuals from their genotype data. Inbreeding coefficients of and relatedness (or kinship coefficient) between individuals are then calculated from the estimated Δ. One method is designed to apply to a small sample or a sample containing a high proportion of close relatives where allele frequencies and their powers or products are poorly estimated by assuming a large sample of non-inbred and unrelated individuals. It adopts an expectation maximisation (EM) algorithm to estimate both Δ and allele frequencies jointly and iteratively. The other method is designed to apply to a large sample of individuals containing few close relatives. It is fast because it, like all previous estimators, estimates Δ only and does not make iterative updates of allele frequencies by accounting for the inferred relatedness through the EM algorithm. EMIBD9 has both methods implemented for multiple computer platforms (Windows, Mac and Linux), and the Windows version has a GUI that facilitates data input and results visualisation. The GUI can also be used to simulate genotype data which are used to investigate factors affecting relatedness estimation accuracy, to optimise the experimental design of a relatedness study, and to compare the performance of different relatedness estimators.