NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees

By Kevin C. Chen, Dannie Durand, Martín Farach-Colton. J. Comput. Biol., 2000

531 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/667eb12510a843f3159cbe6fefa24831af0ed9e7

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Citations in the corpus

Ortholog identification in the presence of domain architecture rearrangement (2011, methodology): “Most phylogenetic orthology prediction methods employ a process called ‘tree reconciliation’, overlaying the gene tree with a trusted species tree, to parsimoniously infer speciation, duplication and gene loss events; examples of these include EnsemblCompara [45], RIO [30], Orthostrapper [46] and NO”
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach (2010, methodology): “With outgroups identified and pruned from the alignment, each gene tree was reconstructed and then reconciled to the metazoan species tree [79] using NOTUNG [80].”
A Hybrid Micro–Macroevolutionary Approach to Gene Tree Reconstruction (2005, unknown): “In a previous study (Chen et al. , 2000), we developed a test set of thirteen trees discussed in three recent articles on large scale duplication (Hughes, 1998; Pebusque et al. , 1998; Ruvinsky and Silver, 1997).”