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Efficient Generation of Uniform Samples from Phylogenetic Trees

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Algorithms in Bioinformatics (WABI 2003)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 2812))

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Abstract

In this paper, we introduce new algorithms for selecting taxon (leaf) samples from large phylogenetic trees, uniformly at random, under certain biologically relevant constraints on the taxa. All the algorithms run in polynomial time and have been implemented.

The algorithms have direct applications to the evaluation of phylogenetic tree and supertree construction methods using biologically curated data.

We also relate one of the sampling problems to the well-known clique problem on undirected graphs. From this, we obtain an interesting new class of graphs for which many open problems exist.

This work was supported by the Natural Sciences and Engineering Research Council of Canada and the Canada Research Chairs Program.

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Author information

Authors and Affiliations

  1. Caprion Pharmaceuticals, 7150 Alexander-Fleming, Montréal, QC, Canada, H4S 2C8

    Paul Kearney

  2. School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada, N2L 3G1

    J. Ian Munro & Derek Phillips

Authors
  1. Paul Kearney
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  2. J. Ian Munro
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  3. Derek Phillips
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Editor information

Editors and Affiliations

  1. Department of Biomathematical Sciences, The Mount Sinai School of Medicine, 10029-6574, New York, NY

    Gary Benson

  2. Institute of Biomedical and Life Sciences, Division of Environmental and Evolutionary Biology, University of Glasgow, G12 8QQ, Glasgow, Scotland

    Roderic D. M. Page

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© 2003 Springer-Verlag Berlin Heidelberg

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Kearney, P., Munro, J.I., Phillips, D. (2003). Efficient Generation of Uniform Samples from Phylogenetic Trees. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_14

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  • DOI: https://doi.org/10.1007/978-3-540-39763-2_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20076-5

  • Online ISBN: 978-3-540-39763-2

  • eBook Packages: Springer Book Archive

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