Pedimap is a tool for exploring and visualizing the flow of phenotypes and alleles (observed or based on Identity-by-Descent calculations) through pedigrees.

Pedimap has tools for the manual and automatic selection of parts of the pedigree based on criteria such as ancestors and/or progeny to a specified number of generations, along the maternal, paternal or both lines, sibs etc. For each selection multiple views can be generated to display different linkage groups, phenotypic traits etc. Once a view is created for one selection, it can be automatically recreated for any other selection. Pedimap can deal with numeric as well as textual phenotypic scores, and with polyploids as well as diploids. The genetic information can be displayed according to genetic linkage maps, hence the name

Pedimap is a useful stand-alone tool to check marker data and to understand the relation between phenotype and genotype. Further, Pedimap can be used to display the results calculated by the FlexQTL software developed by Dr Marco Bink of WUR – Biometris. Pedimap can quickly highlight problematic marker scores and display the calculated Identity-by-Descent information. Pedimap and FlexQTL are designed to work together.

Part of an apple pedigree showing Identity-by-Descent probabilities for chromosome 1. Each color represents a different founder allele. The two rectangles in each individual represent the maternally and paternally inherited chromosome. The vertical dimension of each rectangle corresponds to the positions along the linkage map, while the width of a color at particular height reflects the probability that the corresponding founder allele is present at that locus on the map.

Obtaining Pedimap

Pedimap can be downloaded from GitHub


Pedimap was developed at WUR – Plant Breeding. Its development was started in the framework of the European HiDRAS ( project and continued within USDA-NIFA-RosBREED ( and EU-FruitBreedomics ( projects.