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| Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen, Vincent Moulton, "SuperQ: Computing Supernetworks from Quartets," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 1, pp. 151-160, Jan.-Feb., 2013. | |||
| BibTex | x | ||
| @article{ 10.1109/TCBB.2013.8, author = {Stefan Grünewald and Andreas Spillner and Sarah Bastkowski and Anja Bögershausen and Vincent Moulton}, title = {SuperQ: Computing Supernetworks from Quartets}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {10}, number = {1}, issn = {1545-5963}, year = {2013}, pages = {151-160}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.8}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, } | |||
| RefWorks Procite/RefMan/Endnote | x | ||
| TY - JOUR JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics TI - SuperQ: Computing Supernetworks from Quartets IS - 1 SN - 1545-5963 SP151 EP160 EPD - 151-160 A1 - Stefan Grünewald, A1 - Andreas Spillner, A1 - Sarah Bastkowski, A1 - Anja Bögershausen, A1 - Vincent Moulton, PY - 2013 KW - Phylogeny KW - Vegetation KW - Computational biology KW - Bioinformatics KW - Visualization KW - Data visualization KW - Electronic mail KW - split network KW - Supertree KW - phylogenetic network KW - consensus network KW - supernetwork VL - 10 JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics ER - | |||
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.8
Web Extra: View Supplemental Material(PDF)
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. We compare the performance of SuperQ to the Z-closure and Q-imputation supernetwork methods, and also present an analysis of some published data sets as an illustration of its applicability.
Index Terms:
Phylogeny,Vegetation,Computational biology,Bioinformatics,Visualization,Data visualization,Electronic mail,split network,Supertree,phylogenetic network,consensus network,supernetwork
Citation:
Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen, Vincent Moulton, "SuperQ: Computing Supernetworks from Quartets," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 1, pp. 151-160, Jan.-Feb. 2013, doi:10.1109/TCBB.2013.8
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