AlphaAssign is a parentage assignment algorithm. This program uses a likelihood based model to determine the sire of an individual based on a list of potential sires. AlphaAssign differs from other parentage assignment algorithms by having the option to use phase information to determine parentage.
AlphaBayes is a simple program for genome-wide marker regression along with fixed and random effects. This is a stripped down no-frills version of previous AlpahBayes that only fits a ridge regression model for markers.
AlphaFamImpute is a genotype calling, phasing, and imputation algorithm for large full-sib families in diploid plants and animals which supports individuals genotyped with SNP array or GBS data.
AlphaFamSeq is a family-based phasing algorithm for variable-coverage sequence data that prioritises the minimisation of phasing errors and, conditional on this, maximise the proportion of alleles that are phased. The algorithm uses sequence data and at least three generations pedigree of sequenced individuals.
AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information available. The program uses segregation analysis and haplotype library imputation to impute alleles and genotypes.
AlphaLearn is an R package containing practical exercises used in short courses given by the Hickey group.
AlphaMate is software package for optimising selection, maintenance of diversity, and mate allocation in animal and plant breeding programs.
AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling
AlphaPhase is a software package for phasing genotype data. The program implements methods to determine phase using an extended Long Range Phasing and Haplotype Library Imputation.
AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations.
AlphaRecode is a simple program which will recode a pedigree and sort it with parents coming first before a Individual.
AlphaSeqOpt is a software package for determining the optimum distribution of sequencing resources within a population of interest. AlphaSeqOpt determines which individuals should be prioritised for sequencing and the total investment to be made in sequencing this individual.
AlphaSimR is an R package for simulating plant and animal breeding programs.