NOTUNG: Dating gene duplications using gene family trees

Kevin Chen, Dannie Durand, Martin Farach-Colton

Research output: Contribution to conferencePaperpeer-review

14 Scopus citations

Abstract

Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process. Many studies in the molecular evolution literature have used this approach on small data sets, using analyses performed by hand. The rapid growth of genetic sequence data will soon allow similar studies on a genomic scale but such studies will be limited unless the analysis can be automated. Even existing data sets admit alternative hypotheses that would be too tedious to consider without automation. In this paper, we describe a toolbox called NOTUNG that facilitates large scale analysis, using both rooted and unrooted trees. When tested on trees analyzed in the literature, NOTUNG consistently yielded results that agree with the assessments in the original publications. Thus, NOTUNG provides a basic building block for inferring duplication dates from gene trees automatically and can also be used as an exploratory analysis tool for evaluating alternative hypotheses.

Original languageEnglish (US)
Pages96-106
Number of pages11
StatePublished - 2000
Externally publishedYes
EventRECOMB 2000: 4th Annual International Conference on Computational Molecular Biology - Tokyo, Jpn
Duration: Apr 8 2000Apr 11 2000

Other

OtherRECOMB 2000: 4th Annual International Conference on Computational Molecular Biology
CityTokyo, Jpn
Period4/8/004/11/00

All Science Journal Classification (ASJC) codes

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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