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.

UNPHASED Features:
1. Analysis of nuclear families and unrelated subjects, and combinations of the two
2. Analysis of discrete or quantitative traits
3. Maximum likelihood treatment of missing genotype data and uncertain haplotypes
4. Global association tests and tests of individual haplotypes
5. Conditioning tests that allow for previous associations of linked loci
6. Inclusion of information from additional tag markers
7. Support for non-genetic covariates including parent-of-origin
8. Permutation tests allowing for multiple testing

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.