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A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees

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Bioinformatics Research and Applications (ISBRA 2012)

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

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Abstract

The Robinson-Foulds (RF) distance is a well-established measure for the comparative analysis of phylogenetic trees, and comparing unrooted gene trees with rooted species trees is a standard application in phylogenetics. However, the RF distance is not defined to compare unrooted trees with rooted trees. Here we propose urRF a new measure based on the standard RF distance to compare an unrooted tree with a rooted tree, and describe a linear time algorithm to compute urRF. Further, we show that our measure relates to several intriguing properties that can be crucial for the in-depth comparative study and the credible rooting of trees. Finally, we present detailed empirical studies based on real data sets demonstrating the performance of our novel RF measure, the efficiency of our linear time algorithm and the quality of determining optimal rootings of unrooted gene trees.

Support was provided to PG by the grant of MNiSW #N N301 065236, to OE by the NSF (#0830012 and #106029), and to PG and OE by NCN #2011/01/B/ST6/02777 and the NIMBioS Working Group: Gene Tree Reconciliation through NSF #EF-0832858.

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Author information

Authors and Affiliations

  1. Institute of Informatics, University of Warsaw, Poland

    Paweł Górecki

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

    Oliver Eulenstein

Authors
  1. Paweł Górecki
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  2. 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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Górecki, P., Eulenstein, O. (2012). A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees. 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_12

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  • DOI: https://doi.org/10.1007/978-3-642-30191-9_12

  • 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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