PhenotypeSimulator
R/CRAN framework for simulating genotype to phenotype relationships. It can model multiple traits with multiple underlying genetic loci as well as complex covariate and observational noise structure. This package has been designed to work with many common genetic tools both for input and output.

plinkQC
R/CRAN package for common genotype quality control steps. It provides an easily applicable workflow from per-individual and per-marker quality control to the generation of the new, quality-controlled dataset. The outcomes of each quality control step are summarised in a quality control report.

LiMMBo
Python module for computationally efficient joint genetic analysis of high-dimensional phenotypes, using linear mixed models with bootstrapping.