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Bioinformatics Advance Access published online on October 21, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn523
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

QGene 4.0, an extensible Java QTL-analysis platform

Roby Joehanes 1 and James C. Nelson 1,*

1Department of Plant Pathology, Kansas State University, Manhattan, KS 66506.

*To whom correspondence should be addressed. Dr. James C. Nelson, E-mail: jcn{at}ksu.edu


  Abstract

Summary: Of many statistical methods developed to date for quantitative-trait-locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison, and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing, and haploid-doubling steps; includes map, population, and trait simulators; and is scriptable.

Availability: Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

Contact: jcn{at}ksu.edu

Associate Editor: Dr. Alex Bateman

Received on August 21, 2008; revised on September 26, 2008; accepted on October 4, 2008

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