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2007

Automatic genome-wide reconstruction of phylogenetic gene trees

11 years 9 months ago
Automatic genome-wide reconstruction of phylogenetic gene trees
Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale are still in their infancy. Here, we present SYNERGY, a novel and scalable algorithm that uses sequence similarity and a given species phylogeny to reconstruct the underlying evolutionary history of all genes in a large group of species. In doing so, SYNERGY resolves homology relations and accurately distinguishes orthologs from paralogs. We applied our approach to a set of nine fully sequenced fungal genomes spanning 150 million years, generating a genome-wide catalog of orthologous groups and corresponding gene trees. Our results are highly accurate when compared to a manually curated gold standard, and are robust to the quality of input according to a novel jackknife confidence scoring. The reconstructed gene trees provide a comprehensive view of gene evolution on a genomic scale. Our approach can be app...
Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Reg
Added 02 Oct 2010
Updated 02 Oct 2010
Type Conference
Year 2007
Where ISMB
Authors Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev
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