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FlexQTL for QTL analysis in pedigreed populations

FlexQTL for QTL analysis in pedigreed populations: a software package developed in collaboration with Plant Breeding.

FlexQTL is a software package for Quantitative Trait Loci (QTL) analysis with an emphasis on the known pedigree of a population. Such a population may comprise a single bi-parental mapping population up to complex multi-generations pedigrees.

The software package FlexQTL is based on Bayesian analysis theory and implemented via Markov chain Monte Carlo (MCMC) simulation algorithms, as described in several peer-reviewed publications. This software may be used for

1.     Quantitative Trait Locus (QTL) mapping - To estimate the number of QTL and the position, effect size and individuals’ genotypes for each QTL.

2.     Identity By Descent (IBD) probabilities - To estimate the IBD probability at any given chromosomal position.

Linked to the FlexQTL software, the software package VisualFlexQTL has been recently developed to provide a user-friendly interface to define the parameterization of a FlexQTL analysis and to inspect the numerous output of FlexQTL in a systematic order. The VisualFlexQTL software includes various R scripts to produce charts and tables that visualize and summarize important results such as posterior inference on QTL positions, effect sizes, and individuals’ genotype.


FlexQTL (TM) is available for research applications. Please use the contact button at the top of this page for further information.