Genetic distance for a general non-stationary markov substitution process.

ABSTRACT: The genetic distance between biological sequences is a fundamental quantity in molecular evolution. It pertains to questions of rates of evolution, existence of a molecular clock, and phylogenetic inference. Under the class of continuous-time substitution models, the distance is commonly defined as the expected number of substitutions at any site in the sequence. We eschew the almost ubiquitous assumptions of evolution under stationarity and time-reversible conditions and extend the concept of the expected number of substitutions to nonstationary Markov models where the only remaining constraint is of time homogeneity between nodes in the tree. Our measure of genetic distance reduces to the standard formulation if the data in question are consistent with the stationarity assumption. We app

SUBMITTER: Kaehler BD 

PROVIDER: S-EPMC4380038 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature