Reconciling gene trees with apparent polytomies
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
Evolution of tandemly repeated sequences through duplication and inversion
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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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 result 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.