Improved approximation algorithms for tree alignment
Journal of Algorithms
Inferring evolutionary trees with strong combinatorial evidence
Theoretical Computer Science - computing and combinatorics
Methods for reconstructing the history of tandem repeats and their application to the human genome
Journal of Computer and System Sciences - Computational biology 2002
Reconstructing the Duplication History of a Tandem Repeat
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Simultaneous identification of duplications and lateral transfers
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Comparing Tandem Repeats with Duplications and Excisions of Variable Degree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Evolution of tandemly arrayed genes in multiple species
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Automated segmentation of DNA sequences with complex evolutionary histories
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Alignment of tandem repeats with excision, duplication, substitution and indels (EDSI)
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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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 through simulations that this method improves all existing programs for both reconstructing the topology of the true tree and recovering its duplication events. We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our method than using any other program.