NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Tree. 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.

References in zbMATH (referenced in 13 articles )

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  1. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  2. Huber, K. T.; Scholz, G. E.: Beyond representing orthology relations by trees (2018)
  3. Beretta, Stefano; Dondi, Riccardo: Correcting gene trees by leaf insertions: complexity and approximation (2016)
  4. Beretta, Stefano; Castelli, Mauro; Dondi, Riccardo: Correcting gene tree by removal and modification: tractability and approximability (2015)
  5. Dondi, Riccardo; El-Mabrouk, Nadia; Swenson, Krister M.: Gene tree correction for reconciliation and species tree inference: complexity and algorithms (2014)
  6. Lafond, Manuel; Swenson, Krister M.; El-Mabrouk, Nadia: Error detection and correction of gene trees (2013)
  7. Zheng, Yu; Wu, Taoyang; Zhang, Louxin: A linear-time algorithm for reconciliation of non-binary gene tree and binary species tree (2013)
  8. Dondi, Riccardo; El-Mabrouk, Nadia: Minimum leaf removal for reconciliation: complexity and algorithms (2012)
  9. Scornavacca, C.; Berry, V.; Ranwez, V.: Building species trees from larger parts of phylogenomic databases (2011)
  10. Thomas, Paul D.: GIGA: a simple, efficient algorithm for gene tree inference in the genomic age (2010) ioport
  11. Wehe, André; Chang, Wen-Chieh; Eulenstein, Oliver; Aluru, Srinivas: A scalable parallelization of the gene duplication problem (2010)
  12. Scornavacca, Celine; Berry, Vincent; Ranwez, Vincent: From gene trees to species trees through a supertree approach (2009)
  13. Durand, Dannie; Halldórsson, Bjarni V.; Vernot, Benjamin: A hybrid micro-macroevolutionary approach to gene tree reconstruction (2005)