Clustered SplitsNetworks

  • Lichen Bao
  • Sergey Bereg
Conference paper

DOI: 10.1007/978-3-540-85097-7_44

Part of the Lecture Notes in Computer Science book series (LNCS, volume 5165)
Cite this paper as:
Bao L., Bereg S. (2008) Clustered SplitsNetworks. In: Yang B., Du DZ., Wang C.A. (eds) Combinatorial Optimization and Applications. COCOA 2008. Lecture Notes in Computer Science, vol 5165. Springer, Berlin, Heidelberg

Abstract

We address the problem of constructing phylogenetic networks using two criteria: the number of cycles and the fit value of the network. Traditionally the fit value is the main objective for evaluating phylogenetic networks. However, a small number of cycles in a network is desired and pointed out in several publications.

We propose a new phylogenetic network called CS-network and a method for constructing it. The method is based on the well-known splitstree method. A CS-network contains a face which is k-cycle, k ≥ 3 (not as splitstree). We discuss difficulties of using non-parallelogram faces in splitstree networks. Our method involves clustering and optimization of weights of the network edges.

The algorithm for constructing the underlying graph (except the optimization step) has a polynomial time. Experimental results show a good performance of our algorithm.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Lichen Bao
    • 1
  • Sergey Bereg
    • 1
  1. 1.Department of Computer Science Erik Jonsson School of Engineering & Computer ScienceThe University of Texas at DallasRichardsonUSA

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