IDEAS home Printed from https://ideas.repec.org/p/wop/safiwp/01-01-006.html
   My bibliography  Save this paper

Landscapes on Spaces of Trees

Author

Listed:
  • Oliver Bastert
  • Dan Rockmore
  • Peter F. Stadler
  • Gottfried Tinhofer

Abstract

Combinatorial optimization problems defined on sets of phylogenetic trees are an important issue in computational biology, for instance the problem of reconstruction a phylogeny using maximum likelihood or parsimony approaches. The collection of possible phylogenetic trees is arranged as a so-called Robinson graph by means of the nearest neighborhood interchange move. The coherent algebra and spectra of Robinson graphs are discussed in some detail as their knowledge is important for an understanding of the landscape structure. We consider simple model landscapes as well as landscapes arising from the maximum parsimony problem, focusing on two complementary measures of ruggedness: the amplitude spectrum arising from projecting the cost functions onto the eigenspaces of the underlying graph and the topology of local minima and their connecting saddle points.

Suggested Citation

  • Oliver Bastert & Dan Rockmore & Peter F. Stadler & Gottfried Tinhofer, 2001. "Landscapes on Spaces of Trees," Working Papers 01-01-006, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:01-01-006
    as

    Download full text from publisher

    To our knowledge, this item is not available for download. To find whether it is available, there are three options:
    1. Check below whether another version of this item is available online.
    2. Check on the provider's web page whether it is in fact available.
    3. Perform a search for a similarly titled item that would be available.

    References listed on IDEAS

    as
    1. Wim Hordijk & Peter F. Stadler, 1998. "Amplitude Spectra of Fitness Landscapes," Working Papers 98-02-021, Santa Fe Institute.
    2. Fernando F. Feirreira & José F. Fontanari & Peter F. Stadler, 2000. "Landscape Statistics of the Low Autocorrelated Binary String Problem," Working Papers 00-07-033, Santa Fe Institute.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Christoph Flamm & Ivo L. Hofacker & Peter F. Stadler & Michael T. Wolfinger, 2001. "Barrier Trees of Degenerate Landscapes," Working Papers 01-09-053, Santa Fe Institute.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Christoph Flamm & Ivo L. Hofacker & Peter F. Stadler & Michael T. Wolfinger, 2001. "Barrier Trees of Degenerate Landscapes," Working Papers 01-09-053, Santa Fe Institute.
    2. Dan Rockmore & Peter Kostelec & Wim Hordijk & Peter F. Stadler, 1999. "Fast Fourier Transform for Fitness Landscapes," Working Papers 99-10-068, Santa Fe Institute.
    3. Koutras, M. V. & Tsitmidelis, S. & Zissimopoulos, V., 2003. "Evaluation of reliability bounds by set covering models," Statistics & Probability Letters, Elsevier, vol. 61(2), pages 163-175, January.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:wop:safiwp:01-01-006. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Thomas Krichel (email available below). General contact details of provider: https://edirc.repec.org/data/epstfus.html .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.