- Lichen BaoAffiliated withDepartment of Computer Science Erik Jonsson School of Engineering & Computer Science, The University of Texas at Dallas
- , Sergey BeregAffiliated withDepartment of Computer Science Erik Jonsson School of Engineering & Computer Science, The University of Texas at Dallas
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.
- Clustered SplitsNetworks
- Book Title
- Combinatorial Optimization and Applications
- Book Subtitle
- Second International Conference, COCOA 2008, St. John’s, NL, Canada, August 21-24, 2008. Proceedings
- pp 469-478
- Print ISBN
- Online ISBN
- Series Title
- Lecture Notes in Computer Science
- Series Volume
- Series ISSN
- Springer Berlin Heidelberg
- Copyright Holder
- Springer-Verlag Berlin Heidelberg
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