Models of Genome-Level Mutations
String search, edit, and alignment tools have been extensively used in studies of molecular evolution. However, their use has primarily been aimed at comparing strings representing single genes or single proteins. For example, evolutionary studies have usually selected a single protein and have examined how the amino acid sequence for that protein differs in different species. Accordingly, string edit and alignment algorithms have been guided by objective functions that model the most common types of mutations occurring at the level of a single gene or protein: point mutations or amino acid ...