title: Automatic genome-wide reconstruction of phylogenetic gene trees.
abstract: 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 applied to any set of sequenced eukaryotic species with a known phylogeny, and opens the way to systematic studies of the evolution of individual genes, molecular systems and whole genomes.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Ilan
authors.initials: I
authors.lastname: Wapinski
authors.forename: Avi
authors.initials: A
authors.lastname: Pfeffer
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D014644:Genetic Variation / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*