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| 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.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.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 |