Dprime, SNPGWA and Dandelion

This group comprises three whole genome association tools from Wake Forest University:

Dprime: This tool computes measures of linkage disequilibrium. It reads a data file of individual marker data and computes linkage disequilibrium statistics for all possible pairs of markers in the input file. Specific linkage dis-equilibrium statistics and format are determined by the input data and flags chosen.
SNPGWA: This program reads diallelic marker data for case and control individuals from an input file and performs Hardy-Weinberg, genotypic association, linkage disequilibrium, allelic and two and three marker haplotype tests. Results of each test are written to an output file(s).
Dandelion: This tool reads in a file of cases and controls, and uses the EM algorithm, assuming Hardy-Weinberg equilibrium, to estimate autosomal haplotype frequencies for both groups separately and jointly. Using these maximum likelihood haplotype frequency estimates, a likelihood ratio statistic is computed to determine whether there is heterogeneity in the observed haplotype frequencies between the cases and controls.

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