Structural Approaches to Sequence Evolution

Molecules: Proteins and RNA.- Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example.- Gene3D and Understanding Proteome Evolution.- The Evolution of the Globins: We Thought We Understood It.- The Structurally Constrained Neutral Model of Protein Evolution.- Towards Unifying Protein Evolution Theory.- Molecules: Genomes.- A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering.- Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life.- Phylogenetic Analysis.- Molecular Phylogenetics: Mathematical Framework and Unsolved Problems.- Phylogenetics and Computational Biology of Multigene Families.- SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis.- Networks.- Evolutionary Genomics of Gene Expression.- From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation.- Populations.- Drift and Selection in Evolving Interacting Systems.- Adaptation in Simple and Complex Fitness Landscapes.- Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity.