Mendelsoft

Author : S. De Givry, INRA

MendelSoft is an open source software which detects marker genotyping incompatibilities (Mendelian errors only) in complex pedigrees using weighted constraint satisfaction techniques. The input of the software is a pedigree data with genotyping data at a single locus. The output of the software is a list of individuals for which the removal of their genotyping data restores consistency. This list is of minimum size when the program ends.

Another possibility is to find the most probable consistent correction with respect to a Bayesian formulation of the problem. In this case, the output of the software is a list of individuals for which predicted genotypes differ from their genotyping data and such that the corresponding joint probability for the whole problem is maximum.

The problem, its formulation as a weighted constraint satisfaction problem, and some experimental results on simulated and real large animal pedigrees (up to 129516 individuals) are described in:

M. Sanchez, S. de Givry, and T. Schiex, Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques, In Constraints journal, special issue on bioinformatics, 13(1), 2008.

S. de Givry, I. Palhiere, Z. Vitezica, and T. Schiex, Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques, In ICLP-05 workshop on Constraint Based Methods for Bioinformatics, page 9p., Sitges, Spain, 2005.

See Official website for documentation and download