Software

rrBLUP

rrBLUP is an R package for genomic selection and association mapping. Go to the homepage on CRAN for the latest version and the reference manual. For additional help, consult the tutorials on using rrBLUP for genome-wide prediction or for genome-wide association studies. If you use rrBLUP for a publication, please cite this paper.

LPmerge

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.

GBStools

GBStools is an R package for the analysis of genotyping-by-sequencing (GBS) variants. It is still under development and described in more detail in a manuscript under review. The version posted here has been designed for use with F2 or S1 populations. You can also download a tutorial script and data set illustrating its use in diploid potato. Please contact me if you find bugs or have constructive suggestions for improving the reference manual.

GSdesign

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.