UNPHASED: software for genetic association analysis. UNPHASED is a versatile application for performing genetic association analysis. Some of its more important features are: Analysis of nuclear families and unrelated subjects, and combinations of the two; Analysis of discrete or quantitative traits; Maximum likelihood treatment of missing genotype data and uncertain haplotypes; Global association tests and tests of individual haplotypes; Conditioning tests that allow for previous associations of linked loci; Inclusion of information from additional tag markers; Support for non-genetic covariates; including parent-of-origin; Permutation tests allowing for multiple testing.