| anc2plink | Convert ancestry tracks to PLINK binary |
| ancmark | Per marker ancestry proportions |
| ancplot | Barplot of predictions of ancestry proportions |
| ancsmooth | Smoothing of haplotype ancestry predictions |
| ancsvm | SVM-based predictions of haplotype ancestry |
| anctest | Prediction of haplotype ancestry |
| anctrain | Construction of prototype alleles |
| assoc | Genome-wide association analysis |
| blockgen | Haplotype block generator |
| blockstats | HapBlock statistics |
| compress | Compress phased genotype data |
| exfiles | Example files |
| fast2phase | Convert fastPHASE data into the GHap phase format |
| freq | Compute marker allele frequencies |
| froh | Calculation of genomic inbreeding (FROH) |
| fst | Haplotype-based Fst |
| getHinv | Compute the inverse of H |
| hap2plink | Convert haplotype allele counts to PLINK binary |
| haplotyping | Haplotype genotypes |
| hapstats | Haplotype allele statistics |
| ibd | Estimation of IBD sharing |
| inbcoef | Compute measures of inbreeding |
| karyoplot | Individual chromosome painting |
| kinship | Relationship matrix based on genomic data |
| lmm | Linear mixed model |
| loadhaplo | Load haplotype genotype data |
| loadphase | Load binary phased genotype data |
| loadplink | Load binary PLINK data |
| makefile | Create example input files |
| manhattan | Manhattan plot |
| oxford2phase | Convert Oxford data into GHap phase |
| pedcheck | Summary statistics for pedigree |
| phase2plink | Export phase object to PLINK binary |
| predictblup | Predict BLUP from reference |
| profile | Genomic profile |
| relfind | Find relatives in IBD estimates |
| remlci | Confidence intervals for functions of variance components |
| roh | Detection of runs of homozygosity (ROH) |
| simadmix | Simulate individuals from specified admixture proportions |
| simmating | Simulate individuals from specified matings |
| simpheno | Quantitative trait simulation using real genotype data |
| slice | Get a slice of a GHap object |
| subset | Subset GHap objects |
| varblup | Convert BLUP of individuals into BLUP of variants |
| vcf2phase | Convert VCF data into GHap phase |
