Promoting pluridisciplinary research in computational biology and bioinformatics

From the January/February 2013 Issue

SuperQ: Computing Supernetworks from Quartets

By Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen, Vincent Moulton

Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is not possible to observe with a single tree. Here, we introduce SuperQ, a new method for constructing such supernetworks (SuperQ is freely available at www.uea.ac.uk/computing/superq.). It works by first breaking the input trees into quartet trees, and then stitching these together to form a special kind of phylogenetic network, called a split network. This stitching process is performed using an adaptation of the QNet method for split network reconstruction employing a novel approach to use the branch lengths from the input trees to estimate the branch lengths in the resulting network. Compared with previous supernetwork methods, SuperQ has the advantage of producing a planar network.

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Editorials and Announcements

Announcements

• We are pleased to announce that Ying Xu of the Department of Biochemistry and Molecular Biology and the Institute of Bioinformatics at the University of Georgia is the new Editor in Chief of the IEEE/ACM Transactions on Computational Biology and Bioinformatics starting in 2013.
• eBooks of issues of TCBB can now be downloaded from the Computer Society Digital Library

Editorials

• EIC Editorial by M.-F. Sagot (March/April 2011)
• EIC Editorial by M.-F. Sagot (January/February 2011)

Guest Editorials

• Bioinformatics and Computational Systems Biology (July/August 2012)
• High Performance Computational Systems Biology (May/June 2012)
• Special Section on Bioinformatics Research and Applications (July/August 2011)
• Special Focus on Bioinformatics and Systems Biology (March/April 2011)
• Special Section on Bioinformatics Research and Applications (Oct-Dec 2010)

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TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.

            

Published in cooperation with: IEEE Control Systems Society

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