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


ABSTRACT: 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.

SUBMITTER: McCann A 

PROVIDER: S-EPMC2592249 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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

McCann Angela A   Cotton James A JA   McInerney James O JO  

BMC evolutionary biology 20081112


<h4>Background</h4>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 a  ...[more]

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