GeneRecon software uses coalescent theory for mapping linkage disequilibrium.
GeneRecon is a software package specifically designed for linkage disequilibrium mapping using coalescent theory. The project uses a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping with the aid of high-density marker maps. The software package explicitly models the genealogy of a sample of the case chromosomes in the locus area that may be affected by a disease.
The input data for the analysis is either in the genotype or haplotype form of case and control data. GeneRecon then estimates several parameters, most importantly, the disease position. The software is written in C++ and Guile Scheme, and is available as source code (under the GNU General Public License, GPL), as well as binary versions like Linux RPM files.
The source code is compiled successfully on various Linux and UNIX systems, under OS X, and under Windows with Cygwin. However, binary distributions for platforms other than Linux may not be built without proper access to the right architecture. GeneRecon can be started from the command-line; the input data and analysis parameters are described in one or more configuration scripts written in the Scheme programming language.
To run GeneRecon with the configuration script, the user can enter "generecon input.scm" in the command-line. If required, the user can run "generecon --help" to get a complete list of command-line options accepted by GeneRecon. Additionally, GeneRecon provides a quick guide to running the software, which can be accessed under the "Getting Started" section.
In the latest release, GeneRecon has fixed an incorrect prior on the coalescent tree, which resulted in very long convergence times. This fix has improved both accuracy and number of iterations needed for accurate mapping. Overall, GeneRecon is an excellent software package for linkage disequilibrium mapping, which promises accurate and reliable results even for complex datasets.
The input data for the analysis is either in the genotype or haplotype form of case and control data. GeneRecon then estimates several parameters, most importantly, the disease position. The software is written in C++ and Guile Scheme, and is available as source code (under the GNU General Public License, GPL), as well as binary versions like Linux RPM files.
The source code is compiled successfully on various Linux and UNIX systems, under OS X, and under Windows with Cygwin. However, binary distributions for platforms other than Linux may not be built without proper access to the right architecture. GeneRecon can be started from the command-line; the input data and analysis parameters are described in one or more configuration scripts written in the Scheme programming language.
To run GeneRecon with the configuration script, the user can enter "generecon input.scm" in the command-line. If required, the user can run "generecon --help" to get a complete list of command-line options accepted by GeneRecon. Additionally, GeneRecon provides a quick guide to running the software, which can be accessed under the "Getting Started" section.
In the latest release, GeneRecon has fixed an incorrect prior on the coalescent tree, which resulted in very long convergence times. This fix has improved both accuracy and number of iterations needed for accurate mapping. Overall, GeneRecon is an excellent software package for linkage disequilibrium mapping, which promises accurate and reliable results even for complex datasets.
What's New
Version 1.2: N/A