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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.

Keywords

Short Path Network Construction Phylogenetic Network Network Distance Underlying Graph 
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 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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