Front Cover; Multivariate Analyses of Codon Usage Biases; Copyright; Contents; Acknowledgments; Introduction; Chapter 1. Introduction to Correspondence Analysis; 1.1. Chapter objectives; 1.2. Metric choice; 1.3. Properties; Chapter 2. Global Correspondence Analysis; 2.1. Data set; 2.2. Running global correspondence analysis; 2.3. The missing factor F0; 2.4. First factor; 2.5. Second and third factors; 2.6. Fourth and fifth factors; Chapter 3. Within and Between Correspondence Analysis; 3.1. Running the analyses; 3.2. Synonymous codon usage (WCA); 3.3. Amino acid usage (BCA)
A complete case study with all coding sequences from the bacteria Borrellia burgdorferi illustrates how multivariate analyses reveals evolutionary mechanisms acting at the molecular level. They are either mutationnal (symmetric and asymmetric directionnal mutation pressure) or selective (selection against head-on collisions or linked to gene expressivity or subcellular location)
