title: The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.
abstract: BACKGROUND
  In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.
  
  
  RESULTS
  We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.
  
  
  CONCLUSIONS
  We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.
authors.affiliation: Bioinformatics laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland. angela.mccann@nuim.ie
authors.forename: Angela
authors.initials: A
authors.lastname: McCann
authors.forename: James A
authors.initials: JA
authors.lastname: Cotton
authors.forename: James O
authors.initials: JO
authors.lastname: McInerney
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D020459:Genes, rRNA; D020745:Genome, Archaeal; D023281:Genomics / Q000379:methods*; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S