AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. Focal individuals can be descendants of a bi-parental cross at various levels of selfing or can be parents of one or more bi-parental populations. All information on the model of analysis, input files and their layout, is specified in a single parameter file.
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Gonen S, Wimmer V, Gaynor RC, Byrne E, Gorjanc G, Hickey JM.
A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.
Theor Appl Genet. 2018 Nov;131(11):2345-2357. doi: 10.1007/s00122-018-3156-9. Epub 2018 Aug 4. PMID: 30078163; PMCID: PMC6208939.