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.
What's new in
PedGenie PedGenie Descritpion and Functionality
hapMC hapMC Description and Information
hapConstructor hapConstructor Description and Information
Requirements Java 1.6, Genie.jar, .rgen parameter file and pedigree file(s)
optional files : allele / haplotype frequency file, quantitative data file and linkage parameter file
How to execute java -jar Genie.jar analysis_option rgenfile[.rgen]
Output Report Output Report written to
[.rgen file name].report or [.rgen file name].summary file.
Development Software Requires Java 1.6 for execution.
Genie was written in Java 1.6.
QTDTpval was written in Java 1.4.
GeneCountAlleles was written in Java 1.5
GCHap was written in Java 1.5
.rgen Parameter File Detailed description of .rgen XML file
Example Files All PedGenie, hapMC, hapConstructor and QTDT example files
QTDT Interface PedGenie / QTDT Interface Package
download Download Genie and QTDT Interface packages
To Reference Genie Reference information
Registration Please send name and email address to Steven Backus

Last update : May 5, 2010
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