Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms

  • Paweł Górecki
  • Oliver Eulenstein
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7434)


Gene tree reconciliation problems invoke the minimum number of evolutionary events that reconcile gene evolution within the context of a species tree. Here we focus on the deep coalescence (DC) problem, that is, given an unrooted gene tree and a rooted species tree, find a rooting of the gene tree that minimizes the number of DC events, or DC cost, when reconciling the gene tree with the species tree. We describe an O(n) time and space algorithm for the DC problem, where n is the size of the input trees, which improves on the time complexity of the best-known solution by a factor of n. Moreover, we provide an O(n) time and space algorithm that computes the DC scores for each rooting of the given gene tree. We also describe intriguing properties of the DC cost, which can be used to identify credible rootings in gene trees. Finally, we demonstrate the performance of our new algorithms in an empirical study using data from public databases.


Gene Tree Linear Time Algorithm Star Topology Double Edge Rooted Binary Tree 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Paweł Górecki
    • 1
  • Oliver Eulenstein
    • 2
  1. 1.Department of Mathematics, Informatics and MechanicsUniversity of WarsawPoland
  2. 2.Department of Computer ScienceIowa State UniversityUSA

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