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International Symposium on Bioinformatics Research and Applications

ISBRA 2012: Bioinformatics Research and Applications pp 102–114Cite as

GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7292))

Abstract

Gene tree parsimony (GTP) problems infer species supertrees from a collection of rooted gene trees that are confounded by evolutionary events like gene duplication, gene duplication and loss, and deep coalescence. These problems are NP-complete, and consequently, they often are addressed by effective local search heuristics that perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. Still, GTP problems require rooted input gene trees; however, in practice, most phylogenetic methods infer unrooted gene trees and it may be difficult to root correctly. In this work, we (i) define the first local NNI search problems to solve heuristically the GTP equivalents for unrooted input gene trees, called unrooted GTP problems, and (ii) describe linear time algorithms for these local search problems. We implemented the first NNI based local search heuristics for unrooted GTP problems, which enable analyses for thousands of genes. Further, analysis of a large plant data set using the unrooted NNI search provides support for an intriguing new hypothesis regarding the evolutionary relationships among major groups of flowering plants.

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Author information

Authors and Affiliations

  1. Institute of Informatics, University of Warsaw, Poland

    Paweł Górecki

  2. Department of Biology, University of Florida, USA

    J. Gordon Burleigh

  3. Dept. of Computer Science, Iowa State University, USA

    Oliver Eulenstein

Authors
  1. Paweł Górecki
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  2. J. Gordon Burleigh
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  3. Oliver Eulenstein
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Editor information

Editors and Affiliations

  1. Departments of Bioengineering and Electrical Engineering, University of Texas at Dallas, 75080, Richardson, TX, USA

    Leonidas Bleris

  2. Department of Computer Science and Engineering, University of Connecticut, 06269, Storrs, CT, USA

    Ion Măndoiu

  3. Department of Biological Sciences, Carnegie Mellon University, 15213, Pittsburgh, PA, USA

    Russell Schwartz

  4. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

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© 2012 Springer-Verlag Berlin Heidelberg

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Górecki, P., Burleigh, J.G., Eulenstein, O. (2012). GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_11

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  • DOI: https://doi.org/10.1007/978-3-642-30191-9_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30190-2

  • Online ISBN: 978-3-642-30191-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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