UNPHASED: software for genetic association analysis

The latest version is UNPHASED 3.1.6 (24 Jan 2012)

Downloads

Reference

Please reference the following open access paper when using this software: Dudbridge F (2008) Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data. Hum Hered 66:87-98

Support

Please read in the first instance, direct any enquiries to and report bugs to our support forum.

Full resources for support, review and development are available at the UNPHASED sourceforge pages

UNPHASED is a versatile application for performing genetic association analysis. Its features include:

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

Version 3.1 is now available has three major changes from 3.0.13, inlcuding:

Support for PLINK BED (binary PED) files
Faster algorithm for analysing nuclear families
New method for sibships with two missing parents (faster than the standard analysis with small drop in power)
Changed model for quantitative traits (should give similar results to before, but more efficient when combined with covariates)

License

UNPHASED is released under the GNU General Public License (GPL)

      Copyright (c) 2006-11 Frank Dudbridge
      frank.dudbridge lshtm.ac.uk

      This program is free software; you can redistribute it and/or
      modify it under the terms of the GNU General Public License
      as published by the Free Software Foundation; either version 2
      of the License, or (at your option) any later version.
      This program is distributed in the hope that it will be useful,
      but WITHOUT ANY WARRANTY; without even the implied warranty of
      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      GNU General Public License for more details.