Tassel 4:0: Faster, Larger Diversity Analysis - It's All About the Bits

Once again, the Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) software team has been designing another major release. Currently in beta release, TASSEL 4.0 will raise the bar regarding high-throughput analysis. TASSEL 4.0 can handle data sets of one trillion SNPs. The new bit-wise algorithms will process these data sets faster than ever before. TASSEL is Java software that evaluates genotype and trait associations using the tools of population and quantitative genetics. TASSEL can handle data sets commonly encountered in the plant community, e.g., replicated trials, inbred lines, and complex structured pedigrees. TASSEL also has the latest and statistically most powerful approaches for association mapping in complex populations including both General Linear Model (GLM) and Mixed Linear Model (MLM). There have been several significant improvements since TASSEL version 3.0: 1) a new data structure design facilitating bit-wise algorithms; 2) better support of diploid, heterozygous sequences; 3) consistent handling of all genotypic data sets (i.e. SNPs, text); 4) user friendly improvements to the Alignment Viewer and Filtering Dialogs; 5) and the introduction of XML configuration files for the TASSEL Pipeline. TASSEL is an open source project (www.maizegenetics.net/tassel, sourceforge.net/projects/tassel).