.fastdist               Calculate Genotypic Distances
.fixRotation            Fix strand label rotation across consecutive
                        block-structure columns
.hblock                 Build haplotype blocks from a BMH result matrix
                        (native routine wrapper)
.maf                    Calculate minor allele frequency (MAF)
.o2tH                   Convert a one-row haplotype to a two-row
                        haplotype
.ptr2por                Convert a two-row haplotype per individual to a
                        one-row representation
.simulateHalfsib        Simulate Half-Sibling Genotypes
addSwitch               Add Switches
aio                     All-in-one Phasing
bmh                     Block Partitioning
co                      Crossover Detection
cs                      Chromosome Splitter
fixSW                   Fixing Switch Errors
genotypes               Example Genotype Data Set
groupMatSingle          Grouping a Half-sib Family
hbp                     Haplotype Blocks of Phased Data
hh                      Heatmap of Half-sibs
hsphase-package         Phasing, Pedigree Reconstruction, Sire
                        Imputation and Recombination Events for
                        Half-sib Families
hss                     Half-sib Family Splitter
imageplot               Image Plot of Blocking Structure
impute                  Impute of Low Density SNP Marker to High
                        Density (Paternal Strand)
map                     Example Map File
ohd                     Opposing Homozygote Detection
ohg                     Matrix of Opposing Homozygotes
ohplot                  Opposing Homozygotes Plot
para                    Parallel Analysis of Data
pedigree                Example Pedigree
pedigreeNaming          Fix Pedigree Errors
phf                     Half-sib Family Phasing
pm                      Probability Matrix
pogc                    Parent-Offspring Group Constructor
readGenotype            Read and Check the Genotype File
recombinations          Recombination Number
rplot                   Recombination Plot
rpoh                    Reconstruct Pedigree Based on Matrix of
                        Opposing Homozygotes
ssp                     Sire Imputation and Phasing
switchDetector          Switch Detector
