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Reconciliation with Non-binary Gene Trees Revisited

  • Yu Zheng
  • Louxin Zhang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8394)

Abstract

By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence annotate orthologs and paralogs. However, the currently available reconciliation methods for non-binary gene trees are computationally expensive for being applied on a genomic level. Here, an O(|G| + |S|) algorithm is presented to reconcile an arbitrary gene tree G with its corresponding species tree S, where |·| denotes the number of nodes in the corresponding tree. The improvement is achieved through two innovations: a fast computation of compressed child-image subtrees and efficient reconstruction of irreducible duplication histories.

Keywords

Species Tree Gene Tree Defect Tree Incomplete Lineage Sorting Speciation History 
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 International Publishing Switzerland 2014

Authors and Affiliations

  • Yu Zheng
    • 1
  • Louxin Zhang
    • 1
  1. 1.Department of MathematicsNational University of SingaporeSingapore

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