Admixplot               Plot for True Breed Composition
AlleleFreq              Calculate Allele Frequency
BreedEff_Haplo          True Breeding Value (TBV) estimation according
                        to breed of origin
BreedPopCross           Function for crossing two population with breed
                        effects according to breed of origin
BreedPopSelect          Selecting Population with breed effect
                        according to breed of origin
CalQTLeffect            Calculate QTL effect from file generated from
                        ReadQTL (For QMSim generated files)
Coded_to_Haplo          Recode Coded haplotypes according to breed of
                        origin into 0 and 1 format
DamSample               Select Dams
Ext_Pheno               Extract TBV and Phenotype
GenBreedPop             Generate Population with specific breed effect
GenOnePopulation        Simulate Population
MakeGeno                Make Genotype from Haplotype
MatingPop               Function for mating sire and dam
MutationRate            Adding Mutation
Ped_Pheno               Combine Pedigree and Phenotype data
PopSelect               Selecting Population with selection criteria
                        random, phenotype and true breeding value
PopulationID            Adding Population Code before simulating the
                        population
QMSim_PlinkMAP          Format PLINK MAP file from QMSim
QTL_densityplot         Plot for the QTL effect
QTLeffects              Calculation QTL effects
Random_gametes          Random selection of sire and dam gametes
ReadQTL                 Read QTL file obtained from QMSim
Recode_Haplotype        Recode Haplotype with different breed codes
RecombinationPoint      Add Recombination
Reformat_BLUPF90        Reformat genotype data for BLUPF90 analysis
Rescale                 Rescaling SNP Effect
SireSample              Select Sires
TBV_Haplo               Calculation of True breeding Value (TBV)
TwoPopCross             Function for crossing two populations
Var_PhenoRecords        Generate variance components and phenotypic
                        records
generateHP              Generate Historical Population
generateMAP             Generate MAP file
mapQTLfile              Create combined map and qtl file
plinkped                Generate PLINK pedigree file
plotHaplo               Plot for Haplotype segments
read_qmsim_geno         Read QMSim Marker/QTL Genotype File
recProbplot             Plot for recombination points and recombination
                        probability
trueBreedComp           Calculate True Breed Proportion with coded
                        haplotype
