Approaches and Tools of Analysis

With trillions of base pairs of genomes being sequenced and millions of plants being phenotyped, the analysis approaches for dealing with genotypic, phenotypic data and combining them together to understand the genes controlling traits is complex.  Everyone in our group helps to develop analysis approaches and tools.  Most of our analysis approaches start out an idea and publication, and then the most useful to a community are deployed into easy to use open source software.

Associate Genotype

with Phenotype

DNA Analysis

Statistically relating genotypic and phenotypic variation has been the heart of our lab for many years.  We have developed a couple of the leading edge approaches for genetic mapping with diverse germplasm.

Our group develops approaches to deal with skim sequencing such as Genotyping by sequencing (GBS) data, deeper whole sequencing (WGS and HapMaps), and imputing missing data from these surveys.

Software Tools 

Even the best algorithms are rarely used by the community without translation to easy-to-use software. Our genetic mapping software is available for both Java (TASSEL) and R platforms (GAPIT), and our Genotyping by Sequencing tools are part of TASSEL.  See more about software in Bioinformatics.


of a Genome 

There are 2.3 billion base pairs in the genome, however, each base pair in a different context and many play very different functional and non-functional roles.  We are collaborating with colleagues around the world to annotate every base of the maize genome.