HPlus is a user-friendly software application for estimating haplotype frequencies, inferring individual haplotypes, and most significantly assessing haplotypic associations with various types of phenotypes. HPlus handles bi-allelic genetic markers such as SNPs, and multi-allelic genetic markers such as microsatellites.
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Zhao, Li, Khalid (2003),
“A method for assessing disease associations with SNP haplotypes and environmental variables in case-control“,
American Journal of Human Genetics, 72(5):1231-1250.