Genie is an umbrella tool that provides the user with 3 analysis options: PedGenie, hapMC, and hapConstructor. HapConstructor may also be found as a stand-alone analysis tool (hapContructor). All three of these analysis options are designed to test for association between genetic markers and traits in family studies (the design may also include independent individuals, too).

PedGenie performs genetic association analysis (case-control or transmission disequilibrium tests, TDT) for SNPs in families of arbitrary size and structure. hapMC in analogous to PedGenie, but is for performing haplotype testing of specified haplotypes. hapConstructor is a tool to automatically and iteratively build multi-locus SNP haplotypes, from single SNPs to multi-SNP haplotypes, to establish the most significant association signals.