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. Some of the theory underlying GeneRecon is described in:

High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence. Rannala, B. and Reeve, J.P. (2001). Am. J. Hum. Genet. 69: 159–178.

Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies. Morris, A.P., Whittaker, J.C., and Balding, D.J. (2002). Am. J. Hum. Genet. 70:686–707.

The Icelandic Cancer Project — a population-wide approach to studying cancer. Rafnar, T., Thorlacius, S., Steingrimsson, E., Schierup, M.H., Madsen, J.N., Calian, V., Eldon, B.J., Jonsson, T., Hein, J., and Thorgeirsson, S.S. (2004). Nature Reviews Cancer. 4:488–492.

To cite GeneRecon, please use:

GeneRecon—A coalescent based tool for fine-scale association mapping. Mailund, T. Schierup, M.H. Pedersen, C.N.S. Madsen, J.N. Hein, J. and Schauser, L. Bioinformatics 2006 22 (18): 2317–2318; doi:10.1093/bioinformatics/btl153.

GeneRecon is developed in collaboration between Bioinformatics ApS and Bioinformatics Research Center (BiRC) and released under the GNU General Public License.

GeneRecon is written in C++ and Guile Scheme and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM or Debian files. The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.

The most recent versions can be downloaded below, older versions are available from here.

Binary Distributions

• generecon-1.2.1-1.i386.rpm
• generecon-1.2.0-1.i386.rpm
• generecon-1.1.0-1.i386.rpm

• generecon_1.2.1_i386.deb

The rpm-files were built on Linux Fedora Core 4, and the Debian files on Ubuntu Feisty Fawn. If you have problems installing on other Red Hat or Debian based systems, please let me know.

Source Code Distributions

• generecon-1.2.1.tar.gz
• generecon-1.2.0.tar.gz
• generecon-1.1.0.tar.gz

To build the source files, first uncompress and untar the file, then run 'configure' and finally 'make'. To test that the build was successful, run 'make check'. To install the program, run 'make install'.

    $ tar zxf generecon-version.tar.gz
    $ cd generecon-version
    $ ./configure
    $ make
    $ make check
    $ make install

You will need to install the program, not just build it, for the Scheme modules to load correctly (or manually set the GUILE_LOAD_PATH environment variable, see Getting Started for more details).

For the Gentoo system, Neil Shephard <nshephard -at- gmail.com>, has provided an ebuild package. To use it, unpack it in the appropriate place, e.g. /usr/local/portage, and then run emerge:

    $ cp generecon-ebuild.tar.bz2 /usr/local/portage/
    $ cd /usr/local/portage
    $ tar xjvf generecon-ebuild.tar.bz2
    $ emerge -av genercon 

GeneRecon is started from the command-line; the input data and parameters for the analysis are described in one or more configuration scripts written in the Scheme programming language. Starting GeneRecon with the configuration script input.scm is done as:

    $ generecon input.scm

Run generecon --help to get a complete list of command-line options accepted by GeneRecon, or see Getting Started for a quick guide to running GeneRecon, and the GeneRecon Users' Manual for more details.

Consult the reference manual for a list of the GeneRecon specific Scheme functions.

For bug-reports or feature requests, please use our bug-tracking software.

For comments or questions, please contact Thomas Mailund <mailund@birc.au.dk>, Bioinformatics Research Center (BiRC), University of Aarhus, Høegh-Guldbergsgade 10, DK-8000 Århus C.