title: An index of substitution saturation and its application.
abstract: We introduce a new index to measure substitution saturation in a set of aligned nucleotide sequences. The index is based on the notion of entropy in information theory. We derive the critical values of the index based on computer simulation with different sequence lengths, different number of OTUs and different topologies. The critical value enables researchers to quickly judge whether a set of aligned sequences is useful in phylogenetics. We illustrate the index by applying it to an analysis of the aligned sequences of the elongation factor-1alpha gene originally used to resolve the deep phylogeny of major arthropod groups. The method has been implemented in DAMBE.
authors.affiliation: Department of Biology, University of Ottawa, Ottawa, Ont., Canada. xxia@uottawa.ca
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
authors.forename: Zheng
authors.initials: Z
authors.lastname: Xie
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
authors.forename: Lu
authors.initials: L
authors.lastname: Chen
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment