title: The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data.
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.
authors.affiliation: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.|Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, State College, PA.
authors.forename: Yukako
authors.initials: Y
authors.lastname: Katsura
authors.affiliation: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
authors.forename: Craig E
authors.initials: CE
authors.lastname: Stanley
authors.affiliation: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
authors.forename: Sudhir
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.|Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, State College, PA.
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Nei
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005802:Genes, MHC Class II; D000949:Histocompatibility Antigens Class II / Q000235:genetics; D008322:Mammals / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D011336:Probability; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D000949:Histocompatibility Antigens Class II
keywords: MHC class II β chain genes; bootstrap probability; computer program RESTA.; phylogenetic trees; reliability; stability; subtrees