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Bioinformatics Vol. 19 no. 15 2003
Pages 2002-2003
© 2003 Oxford University Press

Applications Note

GCHap: fast MLEs for haplotype frequencies by gene counting

Alun Thomas

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

Received on November 11, 2002 ; revised on February 24, 2003 ; accepted on March 31, 2003

Summary: 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.

Availability: The Java classes and Javadocs pages for GCHap can be obtained from bioinformatics.med.utah.edu/~alun

Contact: alun{at}genepi.med.utah.edu


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A. Thomas and N. J. Camp
Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting
Bioinformatics, March 15, 2006; 22(6): 771 - 772.
[Abstract] [Full Text] [PDF]


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