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MBE Advance Access published online on November 21, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl180
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted November 15, 2006

Research Article

QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets

Stefan Grüunewald 1 *, Kristoffer Forslund 2, Andreas Dress 3, and Vincent Moulton 4

1 CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, P. R. China
2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden
3 CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, P. R. China, and MPI for Mathematics in the Sciences, Leipzig, Germany
4 School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

* To whom correspondence should be addressed.
Stefan Grüunewald, E-mail: stefan{at}picb.ac.cn


  Abstract

We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net method for network construction. Just as Neighbor-Net, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network. To illustrate the applicability of QNet we apply it to a previously published Salmonella data set. We conclude that QNet can provide a useful alternative to NNet if distance data are not available, or a character based approach is preferred. Moreover, it can be used as an aid for determining when a quartet-based tree building method may or may not be appropriate for a given data set. QNet is freely available for download.

Keywords: Phylogenetic tree; Phylogenetic network; Split network; Neighbor-Net; SplitsTree; Quartet.
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