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    The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods

    McCann, Angela and Cotton, James A. and McInerney, James O. (2008) The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods. BMC Evolutionary Biology, 8 (312). pp. 1-3. ISSN 1471-2148

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    Background: In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present. Results: We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods. Conclusion: We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.

    Item Type: Article
    Additional Information: © 2008 McCann et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Keywords: tree of genomes; genome-phylogeny; reconstruction methods; horizontal gene transfer;
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 6263
    Identification Number:
    Depositing User: Dr. James McInerney
    Date Deposited: 17 Jul 2015 11:08
    Journal or Publication Title: BMC Evolutionary Biology
    Publisher: BioMed Central
    Refereed: Yes
    Funders: Science Foundation Ireland (SFI), Irish Research Council for Science Engineering and Technology (IRCSET)
      Use Licence: This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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