HapCluster++
HapCluster++ 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. HapCluster++ is a C++ implementation of the method described in the paper "Fine Mapping of Disease Genes via Haplotype Clustering" by E.R.B. Waldron, J.C. Whitaker, and D.J. Balding. Genetic Epidemiology. 30: 170–179. (2006).
| Tags | Scientific/Engineering Bioinformatics Medical Science |
|---|---|
| Operating Systems | Mac OS X OS Independent Unix |
| Implementation | C++ |
Recent releases
- 14 Feb 2008 13:52
Release Notes: This version is a port to the SNPFile version 2.0 format.
- 18 Oct 2007 14:00
Release Notes: This version adds an option for restricting the MCMC search to a sub-interval of the full data. This is especially useful for SNPFile data, where the regions can be very wide, but where convergence and mixing can be very poor.
- 13 Aug 2007 04:54
Release Notes: This version changes the --additive option to --allelic (since this is more accurate) and documents the option in the man pages.
- 12 Aug 2007 08:28
Release Notes: This version adds a new likelihood function for (near-)additive disease models, increasing the power for detecting association for such diseases.
- 01 Aug 2007 04:00
Release Notes: This version enables sampling of genotypes of the disease status, writing these samples to a file in the form of a matrix. Missing phenotypes have also been added. Individuals with missing phenotype are clustered together with all other individuals, but they are not used in the likelihood calculation.
mailund_birc
14 Jul 2006 02:52
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