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

*Mol Biol Evol*(2017) 34:718-723.

**Abstract**

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.

**MeSH terms**

Computational Biology methods Computer Simulation MHC Class II Genes Histocompatibility Antigens Class II Mammals Genetic Models Phylogeny Probability Reproducibility of Results DNA Sequence Analysis Software MHC class II beta chain genes computer program RESTA phylogenetic trees reliability subtrees genetics stability bootstrap probability

**Note**

Publication Date: 2017-03-01.