GENECOUNTING is a software of gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data
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.
IQLS (Incomplete-Data Quasi-likelihood Score Test) is a C++ program that performs haplotype frequency estimation and case-control association testing between a binary trait and haplotypes of multiple tightly-linked SNPs. A special feature of IQLS is that both related and unrelated individuals can be included in the case-control sample. The user specifies the number of SNPs in the sliding haplotype window, and for each set of SNPs, the IQLS program computes haplotype frequency estimates and both 1-df and full-df tests for haplotype association with a case-control phenotype. The IQLS software is suitable for case-control haplotype analysis in outbred samples with arbitrary combinations of related and unrelated individuals, including large pedigrees, provided that the relationships are known.