Topological Rearrangements and Local Search Method for Tandem Duplication Trees

—The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch [4]. Many recent studies deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees. In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on duplication trees. We show that restricting the neighborhood defined by the SPR (Subtree Pruning and Regrafting) rearrangement to valid duplication trees, allows exploring the whole duplication tree space. We use these restricted rearrangements in a local search method which improves an initial tree via successive rearrangements. This method is applied to the optimization of parsimony and minimum evolution criteria. We show thro...

• Type: Conference
• Year: 2004
• Where: WABI
• Authors: Denis Bertrand, Olivier Gascuel
• Keywords: Algorithms, Duplication Tree, Duplication Tree Space, Valid Duplication Trees, WABI 2004