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Issue No. 02 - March/April (2011 vol. 8)
ISSN: 1545-5963
pp: 517-535
Ali Tofigh , KTH Royal Institute of Technology, Stockholm
Michael Hallett , McGill University, Montreal
Jens Lagergren , KTH Royal Institute of Technology, Stockholm
The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTL-scenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTL-scenarios is NP-hard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixed-parameter tractable algorithm for finding most parsimonious DTL-scenarios.
Trees, biology and genetics, combinatorial algorithms, graph algorithms.

M. Hallett, A. Tofigh and J. Lagergren, "Simultaneous Identification of Duplications and Lateral Gene Transfers," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. , pp. 517-535, 2010.
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