TASSEL is an open-source software package that uses genetic markers to evaluate associations with traits, identify evolutionary patterns, and analyze linkage disequilibrium. TASSEL integrates data access and management functions with different types of analyses to produce tabular and graphic output. It was created using Java to provide cross-platform capability and ease of deployment.

Data can be input from databases or properly formatted text files. Database connections can be made through a GDPC (Genomic Diversity and Phenotype Connection) web service. Within TASSEL, phenotype, genotype and population structure data from different sources can be joined to create data sets for analysis. SNPs and indels can be extracted from aligned nucleotide sequences and used in subsequent analyses.

For a set of taxa, TASSEL can calculate diversity parameters from aligned sequences. To analyze linkage equilibrium, it can calculate D', r², and p-values for all pairs of markers in a data set. A user can add phenotypic data to marker data and fit linear models to test trait-marker associations. Population structure covariates calculated by the STRUCTURE program can be imported and included in the analysis to adjust for population structure. The jGLiM library within TASSEL provides the methods for specifying and solving linear models.

TASSEL displays analytical results in both tables and graphs. Users can create evolutionary trees and plots of linkage disequilibrium and can easily create histograms, pie charts, and XY plots from tabular data. Output can be saved in a variety of formats.

TASSEL is open source software distributed under the Lesser GNU Public License (LPGL). The Java Web-Start application and source code are available at http://www.maizegenetics.net. In addition, the development project is hosted on Sourceforge.net and collaborators are welcomed.