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Bioinformatics. 2003 Oct 12;19(15):2002-3.

GCHap: fast MLEs for haplotype frequencies by gene counting.

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  • 1Department of Medical Informatics and Center for High Performance Computing, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA.


GCHap quickly finds maximum likelihood estimates (MLEs) of frequencies of haplotypes given genotype information on a random sample of individuals. It uses the gene counting method but by excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.


The Java classes and Javadocs pages for GCHap can be obtained from

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