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| getPed | A function to extract values from a snpMatrix object,snp.support and subject.support | 
| getPlink | Read a PLINK binary data file as a list of chromosomes, genotypes and positions | 
| ld.snp3 | Function to calculate pairwise D', r-squared, but also haplotype frequencies | 
| plot.HMMrelate | R generic plot function used for plotting runHmmld.* functions | 
| print.HMMrelate | prints the results for runHMMld | 
| runHmmld | A function for estimating relatedness between to individuals using SNP data | 
| runHmmld.ped | A function for estimating relatedness between to individuals using SNP data, This function should only be used if you have a 'snpMatrix object' and corrosponding 'subject.support' and 'snp.support' | 
| runHmmld.plink | A function using plink binary data for estimating relatedness between to individuals using SNP data | 
| sim_chr | Program used to generate data |