1. The Beginning of Computational Genomics
2. Finding Sequence Similarities
3. Homology: Can We Get It Right?
4. Getting Ready for the Era of Comparative Genomics: The Importance of Viruses
5. The First Fact of Comparative Genomics: Protein Sequences are Remarkably Resilient in Evolution
6. The Second Fact of Comparative Genomics: Functional Convergence at the Molecular Level
7. Prediction of Function and Reconstruction of Metabolism from Genomic Data: Homology-Based Approaches
8. Prediction of Function and Reconstruction of Metabolism: Post-Homology Approaches
9. Structural Genomics:What Does It Tell Us about Life?
10. How Many Protein Families are There?
11. Phylogenetic Inference and the Era of Complete Genomes
12. Two Stories about Evolution
13. Minimal and Ancestral Genomes
14. Comparative Genomics and Systems Biology