title: Rooting a phylogenetic tree with nonreversible substitution models.
abstract: BACKGROUND
  We compared two methods of rooting a phylogenetic tree: the stationary and the nonstationary substitution processes. These methods do not require an outgroup.
  
  
  METHODS
  Given a multiple alignment and an unrooted tree, the maximum likelihood estimates of branch lengths and substitution parameters for each associated rooted tree are found; rooted trees are compared using their likelihood values. Site variation in substitution rates is handled by assigning sites into several classes before the analysis.
  
  
  RESULTS
  In three test datasets where the trees are small and the roots are assumed known, the nonstationary process gets the correct estimate significantly more often, and fits data much better, than the stationary process. Both processes give biologically plausible root placements in a set of nine primate mitochondrial DNA sequences.
  
  
  CONCLUSIONS
  The nonstationary process is simple to use and is much better than the stationary process at inferring the root. It could be useful for situations where an outgroup is unavailable.
authors.affiliation: Mathematics Department, University of California, 970 Evans Hall, Berkeley, CA 94720, USA. vonbing@math.berkeley.edu
authors.forename: Von Bing
authors.initials: VB
authors.lastname: Yap
authors.forename: Terry
authors.initials: T
authors.lastname: Speed
mesh_terms: D000818:Animals; D002965:Classification / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics; D006801:Humans; D016013:Likelihood Functions; D008954:Models, Biological; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D004272:DNA, Mitochondrial