GCHAP

Record added by Jurg Ott (the original Rockefeller list)

Full Name

Gene Counting method for HAPlotype analysis.

Description

This program finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. 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.

Author

Alun Thomas (email: alun@genepi.med.utah.edu)

URL

Language

Java

Reference

  • Thomas (2003), “GCHap: fast MLEs for haplotype frequencies by gene counting”, Bioinformatics, 19:2002-2003.

  • Thomas (2003), “Accelerated gene counting for haplotype frequency estimation”, Annals of Human Genetics, 67:608-612.

GENEPI.JAR