Technical Abstract: The association mapping of complex traits is becoming the method of choice in plant and animal genetics. In most samples, researchers have to deal with both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling sample structure and background QTL. The software can also analyze diversity among groups of sequences, SNPs, or SSRs. Diversity and linkage disequilibrium statistics can be calculated and visualized graphically. Other features include analyzing insertions/deletions, an intuitive graphical interface, easy integration of phenotypic and genotypic data, methods for missing data and ability to interact with databases.