An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data.

@article{Taylor2004AnAO,
  title={An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data.},
  author={Derek J. Taylor and William H. Piel},
  journal={Molecular biology and evolution},
  year={2004},
  volume={21 8},
  pages={1534-7}
}
Despite the importance of molecular phylogenetics, few of its assumptions have been tested with real data. It is commonly assumed that nonparametric bootstrap values are an underestimate of the actual support, Bayesian posterior probabilities are an overestimate of the actual support, and among-gene phylogenetic conflict is low. We directly tested these assumptions by using a well-supported yeast reference tree. We found that bootstrap values were not significantly different from accuracy… CONTINUE READING