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.

Please report bugs or suggestions on how the program / user interface / manual could be improved or made more user friendly to or or

1.1 Availability

AlphaPlantImpute is available from the AlphaGenes website.
Material available comprises the compiled programs for 64 bit Linux, Windows and Mac OSX machines, together

with this document and a suite of worked examples.

1.2 Conditions of use

AlphaPlantImpute is available to the scientific community free of charge. Users are required, however, to credit its use in any publications. Commercial users should contact John Hickey.

Suggested Citation:

Gonen, S., Wimmer, V., Gaynor, R. C., Gorjanc, G., and Hickey, J. M., (in preparation). A heuris- tic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi- parental plant populations. Crop Science XX:XX

1.3 Disclaimer

While every effort has been made to ensure that AlphaPlantImpute does what it claims to do, there is absolutely no guarantee that the results provided are correct. Use of AlphaPlantImpute is entirely at your own risk!



Because the development of AlphaPlantImpute was funded by a commercial partner there are some restrictions on its use. It is fully and freely available to the academic community. Academics who wish to use it for academic purposes should email John Hickey . Commercial organisations who wish to use it should do likewise to discuss the terms under which it can be shared.


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