title: ProCARs: Progressive Reconstruction of Ancestral Gene Orders.
abstract: BACKGROUND
  In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs).
  
  
  RESULTS
  In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method.
  
  
  CONCLUSIONS
  We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program, written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/.
authors.forename: Amandine
authors.initials: A
authors.lastname: Perrin
authors.forename: Jean-Stéphane
authors.initials: JS
authors.lastname: Varré
authors.forename: Samuel
authors.initials: S
authors.lastname: Blanquart
authors.forename: Aïda
authors.initials: A
authors.lastname: Ouangraoua
mesh_terms: D000465:Algorithms; D000828:Animal Population Groups / Q000235:genetics*; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D010802:Phylogeny; D044382:Population Groups / Q000235:genetics*