| ghap.anc2plink | Convert ancestry tracks to PLINK binary |
| ghap.ancmark | Per marker ancestry proportions |
| ghap.ancplot | Barplot of predictions of ancestry proportions |
| ghap.ancsmooth | Smoothing of haplotype ancestry predictions |
| ghap.ancsvm | SVM-based predictions of haplotype ancestry |
| ghap.anctest | Prediction of haplotype ancestry |
| ghap.anctrain | Construction of prototype alleles |
| ghap.assoc | Association analysis for HapAlleles |
| ghap.blockgen | Haplotype block generator |
| ghap.blockstats | HapBlock statistics |
| ghap.blup | Convert breeding values into BLUP solutions of HapAllele effects |
| ghap.compress | Compress phased genotype data |
| ghap.fast2phase | Convert fastPHASE data into the GHap phase format |
| ghap.freq | Compute marker allele frequencies |
| ghap.fst | Haplotype-based Fst |
| ghap.hap2plink | Convert haplotype allele counts to PLINK binary |
| ghap.haplotyping | Haplotype genotypes |
| ghap.hapstats | Haplotype allele statistics |
| ghap.hslice | Get a slice of the haplo object |
| ghap.karyoplot | Individual chromosome painting |
| ghap.kinship | Kinship matrix from haplotypes |
| ghap.kinv | Inverse of kinship matrix |
| ghap.lmm | Linear mixed model |
| ghap.loadhaplo | Load haplotype genotype data |
| ghap.loadphase | Load binary phased genotype data |
| ghap.makefile | Create example input files |
| ghap.manhattan | Manhattan plot |
| ghap.oxford2phase | Convert Oxford data into GHap phase |
| ghap.pca | Principal Components Analysis |
| ghap.profile | Haplotype allele profile |
| ghap.pslice | Get a slice of the phase object |
| ghap.simpheno | Quantitative trait simulation using real HapGenotype data |
| ghap.subsethaplo | Subset GHap.hapo object |
| ghap.subsetphase | Subset GHap.phase object |
| ghap.vcf2phase | Convert VCF data into GHap phase |