The Division of Genetic Epidemiology utilizes the following software programs to perform genetic analysis:
Genie
A general-purpose tool to analyze association and transmission disequilibrium (TDT) between genetic markers and traits in studies of families and independent individuals. It implements 3 analysis options.
PedGenie
Performs genetic association analysis in studies of families of arbitrary sizes and structure, and independent cases and controls.
hapMC
Performs analysis on haplotype data. It uses Monte Carlo procedure and Expectation-Maximization estimates of haplotypes to provide valid haplotype tests for various standard association statistics.
hapConstructor
Explores multi-locus associations in candidate genes and regions. It automatically builds multi-locus SNP sets to test for association in a case-control framework.
PCAtag
This software is used for Selecting Tagging-SNPs using Principal Component Analysis.
Alun Thomas' Wiki Page
Contains several new programs for modeling linkage disequilibrium and performing shared genomic segment analysis.
If you have any questions about the software we use, please contact Steven Backus at 801-587-9308 or steven.backus@utah.edu.