The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data

Mol Biol Evol. 2017 Mar 1;34(3):718-723. doi: 10.1093/molbev/msw272.


The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here, we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained. We then show that if the tree is to be reliable, both Pb and Ps must be high. We also show that Ps is given by a bootstrap probability of the subtree with the closest outgroup sequence, and computer program RESTA for computing the Pb and Ps values will be presented.

Keywords: MHC class II β chain genes; bootstrap probability; computer program RESTA.; phylogenetic trees; reliability; stability; subtrees.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Computer Simulation
  • Genes, MHC Class II
  • Histocompatibility Antigens Class II / genetics
  • Mammals / genetics
  • Models, Genetic*
  • Phylogeny*
  • Probability
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Software


  • Histocompatibility Antigens Class II