EMIBD9 is a computer program written by Jinliang Wang. It implements a maximum likelihood method to estimate the IBD (Identical By Descent) coefficients between a pair of individuals from their genotype data at some marker loci. It then calculates inbreeding coefficients of and relatedness (kinship coefficients) between individuals from the estimated IBD coefficients.
The method is designed to apply to a small sample of individuals, or a sample containing a substantially high proportion of close relatives. In both cases, allele frequencies and their powers and products are poorly estimated by the current available methods which invariably assume a large sample of noninbred and unrelated individuals.
The method abolishes this assumption and uses an expectation-maximization algorithm to estimate allele frequencies and IBD coefficients jointly. In estimating allele frequencies iteratively, it accounts for both the estimated genetic structure (IBD coefficients) and the small size of the sample. IBD (inbreeding and relatedness) coefficients are iteratively fined by using updated allele frequencies.
The current version (188.8.131.52) of EMIBD9 has the following features:
- Running on all major platforms, Windows, Linux and Mac;
- Allowing for both multiallelic markers (e.g. microsats) and diallelic markers (e.g. SNPs);
- Allowing MPI parallel runs to employ many cores and distributed memory in a cluster;
- Integrated GUI for data input and analysis result visualization (Windows version only);
- Integrating a simulation module to generate genotype data with known familial relationships (Windows version only).