GGT 2.0: Versatile software for visualization and analysis of genetic data

Ever since its first release in 1999, the free software package for visualization of molecular marker data, graphical genotype (GGT), has been constantly adapted and improved. The GGT package was developed in a plant-breeding context and thus focuses on plant genetic data but was not intended to be limited to plants only. The current version has many options for genetic analysis of populations including diversity analyses and simple association studies. A second release of the GGT package, GGT 2.0 (available through http://www.plantbreeding.wur.nl), is therefore presented in this paper. An overview of existing and new features that are available within GGT 2.0, and a case study in which GGT 2.0 is applied to analyze an existing set of plant genetic data, are presented and discussed.