Abstract
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.
This work was supported by MNiSW (#N N301 065236) to PG, by the National Science Foundation (#0830012 and #106029) to OE, and by NCN (#2011/01/B/ST6/02777) and the NIMBioS Working Group “Gene Tree Reconciliation” to PG and OE.
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Górecki, P., Eulenstein, O. (2012). Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms. In: Gudmundsson, J., Mestre, J., Viglas, T. (eds) Computing and Combinatorics. COCOON 2012. Lecture Notes in Computer Science, vol 7434. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32241-9_45
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