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BMCBI
2010

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

9 years 2 months ago
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Background: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict. Results: We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that ...
Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin
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