The analyses include the ability to extract SNPs and indels from alignments and compute a variety of sequence diversity estimates. Diversity estimates include average pairwise divergence (π), segregating sites, and θ (4Nμ), which can be calculated for the entire sequence or by a sliding window. The application also calculates linkage disequilibrium by estimating the standardized disequilibrium coefficient, D’, as well as r², and P-values. TASSEL does association analysis between genotypes and phenotypes by means of a general linear regression model (GLM) and utilizes a logistic regression model for doing associations which include population structure data. It is able to handle genotype data for heterozygotes and can test for additive and dominance effects. There is also basic support for distributing batched analyses among different computers to parallelize processing of large, computationally-intensive jobs.  TASSEL has a variety of utilities including an alignment editor, a network haplotype viewer, a neighbor-joining cladogram generated by neighbor joining, and miscellaneous data graphing and visualization tools. It is open source software written in Java and released under GNU GPL. The application and source code can be downloaded from http://www.maizegenetics.net.