title: Theoretical foundation to estimate the relative efficiencies of the Jukes-Cantor+gamma model and the Jukes-Cantor model in obtaining the correct phylogenetic tree.
abstract: This paper deals with the theoretical foundation to estimate the relative efficiency (probability of inferring the true tree) of different nucleotide substitution models. A novel theoretical approach has been developed to estimate the relative efficiency of nucleotide substitution models based on the neighbor-relation method. The theory was developed directly by using the four-point condition. Initially theoretical formulas for the Jukes-Cantor+gamma (JC+Gamma) model and the Jukes-Cantor (JC) model were developed to estimate their relative efficiencies. Theoretical formulas were used on several model topologies for both models to obtain a true tree. Extensive simulations were performed on the same set of trees to test the strength of the theoretical approach. Simulation results demonstrated a good agreement with results obtained by the theoretical estimation. Overall the theoretical foundation for estimating model efficiencies is very accurate.
authors.affiliation: Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA. anup.som@asu.edu <anup.som@asu.edu>
authors.forename: Anup
authors.initials: A
authors.lastname: Som
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny
chemical_list: D004247:DNA