Genie is 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 for performing genetic association analysis in studies of families of arbitury sizes and structure, and independent cases and controls. hapMC for performing 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 for exploring multi-locus associations in candidate genes and regions. It automatically builds multi-locus SNP sets to test for association in a case-control framework.
Programs Location on Helix
Sample sessions can be downloaded from http://bioinformatics.med.utah.edu/Genie/Examples.html
Say you put the sample files under /home/userID/genie/run1
% java -jar /usr/local/genie/Genie.jar /usr/local/genie/PedGenie /home/userID/genie/run1/SingleGeneCount.rgen