Modeling Sequence Evolution

DNA and amino acid sequences contain information about both the phylogenetic relationships among species and the evolutionary processes that caused the sequences to divergence. Mathematical and statistical methods try to detect this information to determine how and why DNA and protein molecules work the way they do. This chapter describes some of the models of evolution of biological sequences most widely used. It first focuses on single nucleotide/amino acid replacement rate models. Then it discusses the modelling of evolution at gene and protein module levels. The chapter concludes with speculations about the future use of molecular evolution studies using genomic and proteomic data.