TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) is a software package for evaluating trait associations, evolutionary patterns, and linkage disequilibrium in genetic data. It is designed to handle the diversity of data types and sizes common in modern genomics, including a variety of genotype and phenotype file formats.
| Build | Version |
|---|---|
| Latest stable |  |
| Latest nightly |  |
Nightly builds are automated, unreleased snapshots of the develop branch,
published for testing only. They are not versioned releases and are never
published to Maven Central. Use the latest stable release for real work.
If you want to build this from the source, TASSEL needs Java 21.
A Gradle wrapper (./gradlew) is included, so a local Gradle installation is
not required. A native BLAS library (OpenBLAS) is optional but
recommended for fast matrix operations.
Build the runnable JAR and launch the graphical interface:
./gradlew build # assemble build/libs/sTASSEL.jar
./gradlew run # launch the GUIFor prerequisites (including OpenBLAS setup), command-line pipelines, and the standalone distribution, see the documentation links below.
Full documentation lives on the TASSEL docs site:
| Resource | Description |
|---|---|
| Getting Started & Installation | Install the desktop app, standalone distribution, JVM library, or rTASSEL. |
| User Manual | GUI reference for every analysis, filter, and data operation. |
| Pipelines | Command-line pipeline documentation for scripted and batch workflows. |
| Developer Guide | Build from source, architecture, plugin development, testing, and releasing. |
| Contributing | Git workflow, pull requests, and code review. |
| Version History | Release notes and changelog. |
To preview the site locally, run pip install mkdocs-material mkdocs-macros-plugin
followed by mkdocs serve.
Start from the branch that matches your change: develop for features and
non-urgent fixes, main for hotfixes and documentation-only changes.
Documentation changes take a shortcut — they skip the test suite and publish
without cutting a release. See
Contributing
for the full workflow.
If you use TASSEL in your research, please cite the 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.
BibTeX entry:
@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/btm311},
url = {https://academic.oup.com/bioinformatics/article/23/19/2633/185151}
}TASSEL is licensed under the Apache License, Version 2.0.