NOTUNG: A program for dating gene duplications and optimizing gene family trees

K. Chen, D. Durand, M. Farach-Colton

    Research output: Contribution to journalArticlepeer-review


    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 program 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)
    Pages (from-to)429-447
    Number of pages19
    JournalJournal of Computational Biology
    Issue number3-4
    StatePublished - 2000


    • Duplication/loss models
    • Evolutionary tree
    • Gene duplication
    • Gene family
    • Phylogeny

    ASJC Scopus subject areas

    • Modeling and Simulation
    • Molecular Biology
    • Genetics
    • Computational Mathematics
    • Computational Theory and Mathematics


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