A toolset plant3G written with Python and R was designed to conduct GWA (genome-wide analysis), GEP (genomic-enable prediction) and GE (genome evolution) in plants. It combines many functions in a command line package, including SNP manipulation, SNP imputation from high density parental panels to progenies and conducting genome-wide studies with different approaches. See the project homepage for usage details and examples.
Copy the piece of python code to the directory in your $PATH: for example:
$: cp impute4diallel/impute4diallel.py ~/bin/impute4diallel
Then, you will be ready to run it
$: impute4diallel -help
This package is free and open source, licensed under GPL.