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MBE Advance Access originally published online on November 21, 2006
Molecular Biology and Evolution 2007 24(2):532-538; 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

Research Articles

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

Stefan Grünewald*, Kristoffer Forslund{dagger}, Andreas Dress*,{ddagger} and Vincent Moulton§

* Chinese Academy of Science-Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
{dagger} Stockholm Bioinformatics Center, Albanova, Stockholm University, Stockholm, Sweden
{ddagger} Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
§ School of Computing Sciences, University of East Anglia, Norwich, United Kingdom

E-mail: stefan{at}picb.ac.cn.

Accepted for publication November 15, 2006.

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 (NNet) method for network construction. Just as NNet, 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.

Key Words: phylogenetic tree • phylogenetic network • split network • Neighbor-Net • SplitsTree • quartet

William Martin, Associate Editor.


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