Inferring species trees from gene duplication episodes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Linear-Time Algorithms for the Multiple Gene Duplication Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
A linear time algorithm for error-corrected reconciliation of unrooted gene trees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Deciphering the location of gene duplications and multiple gene duplication episodes on the Tree of Life is fundamental to understanding the way gene families and genomes evolve. The multiple gene duplication problem provides a framework for placing gene duplication events onto nodes of a given species tree, and detecting episodes of multiple gene duplication. One version of the multiple gene duplication problem was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed for this problem, but no exact algorithms were known. Results: In this article we solve this longstanding open problem by providing the first exact and efficient solution. We also demonstrate the improvement offered by our algorithm over the best heuristic approaches, by applying it to several simulated as well as empirical datasets. Contact: oeulenst@cs.iastate.edu