Beyond Galled Trees - Decomposition and Computation of Galled Networks

  • Daniel H. Huson
  • Tobias H. Klöpper
Conference paper

DOI: 10.1007/978-3-540-71681-5_15

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4453)
Cite this paper as:
Huson D.H., Klöpper T.H. (2007) Beyond Galled Trees - Decomposition and Computation of Galled Networks. In: Speed T., Huang H. (eds) Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453. Springer, Berlin, Heidelberg

Abstract

Reticulate networks are a type of phylogenetic network that are used to represent reticulate evolution involving hybridization, horizontal gene transfer or recombination. The simplest form of these networks are galled trees, in which all reticulations are independent of each other. This paper introduces a more general class of reticulate networks, that we call galled networks, in which reticulations are not necessarily independent, but may overlap in a tree-like manner. We prove a Decomposition Theorem for these networks that has important consequences for their computation, and present a fixed-parameter-tractable algorithm for computing such networks from trees or binary sequences. We provide a robust implementation of the algorithm and illustrate its use on two biological datasets, one based on a set of three gene-trees and the other based on a set of binary characters obtained from a restriction site map.

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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Daniel H. Huson
    • 1
  • Tobias H. Klöpper
    • 1
  1. 1.Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 TübingenGermany

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