title: Efficient Gene Tree Correction Guided by Genome Evolution.
abstract: BACKGROUND
  Gene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches. Information for their full resolution may lie in the dependency between gene families and their genomic context. Integrative methods, using species tree information in addition to sequence information, often rely on a computationally intensive tree space search which forecloses an application to large genomic databases.
  
  
  RESULTS
  We propose a new method, called ProfileNJ, that takes a gene tree with statistical supports on its branches, and corrects its weakly supported parts by using a combination of information from a species tree and a distance matrix. Its low running time enabled us to use it on the whole Ensembl Compara database, for which we propose an alternative, arguably more plausible set of gene trees. This allowed us to perform a genome-wide analysis of duplication and loss patterns on the history of 63 eukaryote species, and predict ancestral gene content and order for all ancestors along the phylogeny.
  
  
  BACKGROUND
  A web interface called RefineTree, including ProfileNJ as well as a other gene tree correction methods, which we also test on the Ensembl gene families, is available at: http://www-ens.iro.umontreal.ca/~adbit/polytomysolver.html. The code of ProfileNJ as well as the set of gene trees corrected by ProfileNJ from Ensembl Compara version 73 families are also made available.
authors: Département d'Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada.
authors: Emmanuel
authors: E
authors: Noutahi
authors: LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France.
authors: Magali
authors: M
authors: Semeria
authors: Département d'Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada.
authors: Manuel
authors: M
authors: Lafond
authors: Département d'Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada.
authors: Jonathan
authors: J
authors: Seguin
authors: LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France.
authors: Bastien
authors: B
authors: Boussau
authors: LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France.
authors: Laurent
authors: L
authors: Guéguen
authors: Département d'Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada.
authors: Nadia
authors: N
authors: El-Mabrouk
authors: LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France.|INRIA Grenoble Rhône-Alpes, F-38334 Montbonnot, France.
authors: Eric
authors: E
authors: Tannier
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D005796:Genes / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA