Genetics Check Data Contents Verify Gender of Samples Create Annotation Analysis Group Variable Subset and Reorder Genetic Data Recode Genotypes Recode Missing Genotypes Standardize Genotypes Expand Multiallelic Genotypes Flip Strand SNP Power Kinship Matrix Relationship Matrix K Matrix Compression Calculate Square Root of Matrix IBS Sharing Regions Population Measures Phenotype Summary Marker Properties Missing Genotype by Trait Summary LD Block Creation Linkage Disequilibrium LD tagSNP Selection Malecot LD Map Case-Control Association PCA for Population Stratification SNP-Trait Association Imputed SNP-Trait Association Survey SNP-Trait Association Quantitative TDT TDT GWAS Meta-Analysis Multiple SNP-Trait Association Rare Variant Association Pleiotropic Association Marker-Trait Association SNP-SNP Interactions SNP Interaction Discovery Q-K Model Fitness Q-K Mixed Model Haplotype Estimation Haplotype Trend Regression Haplotype Q-K Mixed Model htSNP Selection Affected Sib-Pair Tests Haseman-Elston Regression Variance Components Recombination and Linkage Groups Linkage Map Order Linkage Map Viewer Compare Linkage Maps Build Consensus Linkage Map QTL Single Marker Analysis Build Genotype Probability Data Set QTL IM, CIM and MIM Analysis Compare QTL Plots GxE Interaction Cross Evaluation Progeny Simulation