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Bioinformatics Advance Access originally published online on June 22, 2007
Bioinformatics 2007 23(19):2633-2635; doi:10.1093/bioinformatics/btm308
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

TASSEL: software for association mapping of complex traits in diverse samples

Peter J. Bradbury 1,{dagger},*, Zhiwu Zhang 2,{dagger}, Dallas E. Kroon 2,{dagger}, Terry M. Casstevens 2, Yogesh Ramdoss 3 and Edward S. Buckler 1,2

1United States Department of Agriculture-Agricultural Research Service, 2Institute for Genomic Diversity, Cornell University, Ithaca, New York and 3Cisco Systems, RTP, NC, USA

*To whom correspondence should be addressed.


  Abstract

Summary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.

Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www.maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel.

Contact: pjb39{at}cornell.edu

Associate Editor: Martin Bishop

{dagger}The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.

Received on March 26, 2007; revised on May 11, 2007; accepted on June 2, 2007

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