Newer software packages (polyBreedR, diaQTL, GWASpoly) are being developed and maintained at GitHub.
FIELDimageR is maintained at the GitHub site of OpenDroneMap.
rrBLUP is an R package for genome-wide prediction and GWAS. Go to the homepage on CRAN for the latest version and the reference manual. For additional help with genome-wide prediction, check out this tutorial. Please cite our publication if you use the software. If you are primarily interested in GWAS, try the GWASpoly package, which has better GWAS functionality, works for any ploidy level, and utilizes rrBLUP for the mixed model analysis.
LPmerge is an R package for building consensus maps across multiple populations through linear programming (LP). Please cite the published manuscript if you use the software, which can be downloaded from CRAN. The following tutorial illustrates how to use LPmerge with a real barley dataset.
GSdesign is an R package in the early stages of development. At the moment it includes a function for designing preliminary yield trials with genome-wide markers. If you use GSdesign for a publication, please cite this paper. The source package and reference manual can be downloaded here.