ghap.ancestral          Inference of haplotype origin
ghap.assoc              Association analysis for HapAlleles and
                        HapBlocks
ghap.blmm               Bayesian linear mixed model
ghap.blockgen           Haplotype block generator
ghap.blockstats         Block statistics
ghap.blup               Convert breeding values into BLUP solutions of
                        HapAllele effects
ghap.fst                Haplotype Fst
ghap.hap2tped           Convert haplotype allele counts to PLINK tped
ghap.haplotyping        Haplotype genotypes
ghap.hapstats           Haplotype statistics
ghap.kinship            Kinship matrix from haplotypes
ghap.lmm                Frequentist linear mixed model
ghap.loadhaplo          Load haplotype genotype data
ghap.loadphase          Load phased genotype data
ghap.maf                Compute marker minor allele frequencies
ghap.makefile           Create example input files
ghap.mergehaplo         Merging GHap.haplo objects
ghap.mergephase         Merging GHap.phase objects
ghap.mme                Mixed linear model solver
ghap.outhaplo           Output GHap.haplo object to a file
ghap.outphase           Output GHap.phase object to a file
ghap.pca                Principal Components Analysis
ghap.profile            Haplotype allele profile
ghap.simpheno           Quantitative trait simulation using real
                        HapGenotype data
ghap.subsethaplo        Subset GHap.hapo object
ghap.subsetphase        Subset GHap.phase object
