title: Phylogenetic trees based on gene content.
abstract: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known 'fact' that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method.
  
  
  BACKGROUND
  http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html
authors.affiliation: Center for Bioinformatics, Tübingen University, Sand 14, 72076 Tübingen, Germany. huson@informatik.uni-tuebingen.de
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
authors.forename: Mike
authors.initials: M
authors.lastname: Steel
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D019143:Evolution, Molecular; D014644:Genetic Variation; D016013:Likelihood Functions; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*