UNPHASED is an application for performing genetic association analysis in nuclear families and unrelated subjects. It implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes. Many of the commonly performed analyses are provided including transmission/disequilbrium tests, global and individual tests for haplotypes, tests that account for associations of nearby loci, tests of gene-gene interaction, adjustments for environmental covariates, genotype tests, comparison of risk between different haplotypes, and permutation tests.
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Dudbridge F (2008)
Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data.
Hum Hered 66:87-98