@article{4347,
  abstract     = {Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.},
  author       = {Huelsenbeck, John and Bollback, Jonathan P and Levine, Amy},
  issn         = {0039-7989},
  journal      = {Systematic Biology},
  number       = {1},
  pages        = {32 -- 43},
  publisher    = {Oxford University Press},
  title        = {{Inferring the root of a phylogenetic tree}},
  doi          = {10.1080/106351502753475862},
  volume       = {51},
  year         = {2002},
}

@article{3440,
  abstract     = {Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis.
},
  author       = {Huelsenbeck, John and Bollback, Jonathan P},
  issn         = {0039-7989},
  journal      = {Systematic Biology},
  number       = {3},
  pages        = {351 -- 366},
  publisher    = {Oxford University Press},
  title        = {{Empirical and hierarchical Bayesian estimation of ancestral states}},
  doi          = {10.1080/10635150119871},
  volume       = {50},
  year         = {2001},
}