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Online Consensus and Agreement of Phylogenetic Trees

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Book cover Algorithms in Bioinformatics (WABI 2004)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3240))

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Abstract

Computational heuristics are the primary methods for reconstruction of phylogenetic trees on large datasets. Most large-scale phylogenetic analyses produce numerous trees that are equivalent for some optimization criteria. Even using the best heuristics, it takes significant amount of time to obtain optimal trees in simulation experiments. When biological data are used, the score of the optimal tree is not known. As a result, the heuristics are either run for a fixed (long) period of time, or until some measure of a lack of improvement is achieved. It is unclear, though, what is a good criterion for measuring this lack of improvement. However, often it is useful to represent the collection of best trees so far in a compact way to allow scientists to monitor the reconstruction progress. Consensus and agreement trees are common such representations. Using existing static algorithms to produce these trees increases an already lengthy computational time substantially. In this paper we present efficient online algorithms for computing strict and majority consensi and the maximum agreement subtree.

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Authors and Affiliations

  1. Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA

    Tanya Y. Berger-Wolf

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  1. Tanya Y. Berger-Wolf
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Editors and Affiliations

  1. Department of Informatics and Computational Biology Unit, HIB, University of Bergen, 5020, Bergen, Norway

    Inge Jonassen

  2. Department of Biology,, Penn Center for Bioinformatics, Penn Genomics Institute, 415 S. University Ave., PA 19104, Philadelphia, USA

    Junhyong Kim

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© 2004 Springer-Verlag Berlin Heidelberg

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Berger-Wolf, T.Y. (2004). Online Consensus and Agreement of Phylogenetic Trees. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_30

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  • DOI: https://doi.org/10.1007/978-3-540-30219-3_30

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-23018-2

  • Online ISBN: 978-3-540-30219-3

  • eBook Packages: Springer Book Archive

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