1. The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.
- Author
-
McCann A, Cotton JA, and McInerney JO
- Subjects
- Algorithms, Computational Biology methods, Databases, Genetic, Gene Transfer, Horizontal, Genes, rRNA, Likelihood Functions, Models, Genetic, RNA, Ribosomal, 16S genetics, Sequence Alignment, Sequence Analysis, DNA, Evolution, Molecular, Genome, Archaeal, Genomics methods, Phylogeny
- 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.
- Published
- 2008
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