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.
Highlights
ArticleThe purpose of this article is to examine the reliability of an inferred tree from empirical data
To make our question concrete, let us consider the phylogenetic tree representing the evolution of major histocompatibility complex (MHC)
MHC genes can be classified into class I
Summary
ArticleThe purpose of this article is to examine the reliability of an inferred tree from empirical data. Some interior branches have high Pb values, whereas the others do not. Even if Pb is high, some parts of the tree may not be so reliable as we wish because the Pb value merely represents the probability of partitioning of the entire sequences at the relevant interior branch (Nei and Kumar 2000).
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