Projects / GeneRecon


GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.

Operating Systems

Recent releases

  •  04 Apr 2006 21:59

    Release Notes: This version fixes a bug introduced in the previous release: part of the caching was disabled, leading to a degrade in running time. This release has the caching enabled again.

    •  02 Apr 2006 14:19

      Release Notes: This version fixes an incorrect prior on the coalescent tree that resulted in very long convergence times. The fix greatly improves both accuracy and number of iterations needed for accurate mapping.

      •  20 Mar 2006 18:11

        Release Notes: This release adds a number of new features, including options for setting the weight of the proposed changes, modelling background haplotypes as a first-order Markov chain, and setting a temperature for the MCMC.

        •  06 Mar 2006 16:23

          Release Notes: This version removes hard-wired paths in the source to enable local installations through the configure option --prefix.

          •  12 Feb 2006 14:38

            Release Notes: The beta testing phase is over, and this release fixes the few bugs that were found.

            Recent comments

            20 Jul 2006 00:32 mailund_birc

            GeneRecon in Bioinformatics
            An applicaition note on GeneRecon:

            GeneRecon—A coalescent based tool for fine-scale association mapping

            T. Mailund, M.H. Schierup, C.N.S. Pedersen, J.N. Madsen, J. Hein, and L. Schauser

            has been accepted at Bioinformatics. Advanced access at: doi:10.1093/bioinformatics/btl153. (


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