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Erschienen in:
2008 | OriginalPaper | Buchkapitel
A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes
verfasst von : Xintao Wei, Lenore Cowen, Carla Brodley, Arthur Brady, D. Sculley, Donna K. Slonim
Erschienen in: Bioinformatics Research and Applications
Verlag: Springer Berlin Heidelberg
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As the number of sequenced genomes has grown, we have become increasingly aware of the impact of horizontal gene transfer on our understanding of genome evolution. Methods for detecting horizontal gene transfer from sequence abound. Among the most accurate are methods based on phylogenetic tree inference, but even these can perform poorly in some cases, such as when multiple trees fit the data equally well. In addition, they tend to be computationally intensive, making them poorly suited to genomic-scale applications. We introduce a new method for detecting horizontal transfer that incorporates the
distances
typically used by phylogeny-based methods, rather than the trees themselves. We demonstrate that the distance method is scalable and that it performs well precisely in cases where phylogenetic approaches struggle. We conclude that a distance-based approach may be a valuable addition to the set of tools currently available for identifying horizontal gene transfer.