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Unifying Parsimonious Tree Reconciliation

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Book cover Algorithms in Bioinformatics (WABI 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8126))

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Abstract

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n 2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym .

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Author information

Authors and Affiliations

  1. Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, 04109, Leipzig, Germany

    Nicolas Wieseke, Matthias Bernt & Martin Middendorf

Authors
  1. Nicolas Wieseke
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  2. Matthias Bernt
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  3. Martin Middendorf
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Editor information

Editors and Affiliations

  1. ithree institute,, University of Technology Sydney, 2007, Ultimo, NSW, Australia

    Aaron Darling

  2. Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany

    Jens Stoye

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Wieseke, N., Bernt, M., Middendorf, M. (2013). Unifying Parsimonious Tree Reconciliation. In: Darling, A., Stoye, J. (eds) Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science(), vol 8126. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40453-5_16

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  • DOI: https://doi.org/10.1007/978-3-642-40453-5_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-40452-8

  • Online ISBN: 978-3-642-40453-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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