TASSEL 5

Trait Analysis by aSSociation, Evolution and Linkage

A powerful, open software package for evaluating trait associations, evolutionary patterns, and linkage disequilibrium.

Download Getting Started GitHub

Powerful association mapping

General Linear Model (GLM) and Mixed Linear Model (MLM) approaches. MLM (Nature Genetics) reduces Type I error in complex pedigrees and population structures.

Explore the models

Bit-level speed

Bit-encoded nucleotides make genetic distance and linkage disequilibrium estimates 20–50× faster.

Indel aware

First-class support for insertions & deletions, a dominant form of polymorphism in species like maize.

Download TASSEL 5

Native installers for macOS, Windows, and Linux, plus the standalone command-line distribution.

Go to downloads

Built for GBS

Extract and call SNPs from massive Genotyping-by-Sequencing datasets — tested at 60,000 samples × 2.5M SNPs.

Getting Started

Install TASSEL, explore the user manual and pipelines, and download test data to follow along.

Get started

About TASSEL 5

TASSEL is a software package to evaluate trait associations, evolutionary patterns, and linkage disequilibrium. Strengths of this software:

  1. It provides powerful statistical approaches for association mapping such as General Linear Model (GLM) and Mixed Linear Model (MLM). MLM is a method described in a Nature Genetics paper - Unified Mixed-Model Method for Association Mapping - that reduces Type I error in complex pedigrees and population structures.
  2. TASSEL supports a wide range of indels (insertions & deletions), which are commonly ignored by other software. This is crucial in species like maize where indels are a dominant form of polymorphism.
  3. Bit level encoding of nucleotides so genetic distance and linkage disequilibrium estimates can be made very quickly (20-50X speed increases).
  4. Tools for extracting and calling SNPs from extensive Genotyping-by-Sequencing data (tested for 60,000 samples by over 2.5 million SNPs and 96 million sequence alleles).

Gallery

Citation

Overall Package

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635.

For BibTeX users:

@article{Bradbury2007,
  author  = {Bradbury, Peter J. and Zhang, Zhiwu and Kroon, Dallas E. and Casstevens, Terry M. and Ramdoss, Yogesh and Buckler, Edward S.},
  title   = {{TASSEL}: Software for association mapping of complex traits in diverse samples},
  journal = {Bioinformatics},
  volume  = {23},
  number  = {19},
  pages   = {2633--2635},
  year    = {2007},
  doi     = {10.1093/bioinformatics/btm308},
  url     = {https://doi.org/10.1093/bioinformatics/btm308}
}

Looking for older versions of TASSEL?

Archived versions of TASSEL (versions 3 and 4) can be found on our releases page.

Looking for additional help?

We recommend first searching the archives and posting questions on the Google Discussion Group. If you are on GitHub, we also have a discussion forum on the TASSEL code repository.

Acknowledgements

TASSEL development has been generously supported by the USDA-ARS and the NSF.

TASSEL 5