Multivariate Analyses of Codon Usage Biases

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).

The main objective is to provide a complete and reproducible example of the power of multivariate analyses in this application field

1. Introduction to correspondence analysis 2. Global codon usage 3. Synonymous codon usage 4. Non-synonymous codon usage 5. Within and between-group variability decomposition