GeneRecon--a coalescent based tool for fine-scale association mapping

Thomas Mailund; Mikkel H Schierup; Christian N S Pedersen; Jesper N Madsen; Jotun Hein; Leif Schauser

doi:10.1093/bioinformatics/btl153

GeneRecon--a coalescent based tool for fine-scale association mapping

Bioinformatics. 2006 Sep 15;22(18):2317-8. doi: 10.1093/bioinformatics/btl153. Epub 2006 Apr 21.

Authors

Thomas Mailund¹, Mikkel H Schierup, Christian N S Pedersen, Jesper N Madsen, Jotun Hein, Leif Schauser

Affiliation

¹ Bioinformatics Research Center, University of Aarhus Høegh-Guldbergs Gade 10, DK-8000 Arhus C, Denmark. [email protected]

PMID: 16632491
DOI: 10.1093/bioinformatics/btl153

Abstract

GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case-control data from phased or unphased SNP and microsatellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis-Hastings sampling in the state space of genealogies. Input format, search strategy and the sampled statistics can be configured through the Guile Scheme programming language embedded in GeneRecon, making GeneRecon highly configurable.

Availability: The source code for GeneRecon, written in C++ and Scheme, is available under the GNU General Public License (GPL) at http://www.birc.au.dk/~mailund/GeneRecon

Contact: [email protected].

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Chromosome Mapping / methods*
DNA Mutational Analysis / methods*
Genetic Linkage / genetics
Genetic Predisposition to Disease / genetics*
Genetics, Population*
Humans
Linkage Disequilibrium / genetics*
Models, Genetic*
Models, Statistical
Sequence Analysis, DNA / methods
Software*