1. Fundamentals of molecular evolution: Overview: genes and gene structure; genetic code; mutations and their consequences: changes in the DNA sequence.
2. Molecular evolution of amino acid sequences: amino acid differences and proportion of different amino acids; amino acid substitution matrix.
3. Molecular evolution of DNA sequences: nucleotide differences between sequences; nucleotide substitution in DNA sequences: Jukes-Cantor's one parameter model, Kimura's two parameter model.
4. Sequence alignments for molecular phylogenetics: pairwise alignments; local and global alignments; substitution matrices; dot-plot, dynamic programming algorithm.
5. Multiple alignments: extension of dynamic programming; hidden Markov models; genetic algorithm in multiple alignment.
6. Molecular phylogenetics I: basic classification; molecular systematics; character and distance based methods; tree building and analysis methods (Bayes method; Markov Chain Monte Carlo method, Metropolis criterium).
7. Molecular phylogenetics II: distance methods.
8. Molecular phylogenetics III: maximum parsimony methods.
9. Molecular phylogenetics IV: maximum likelihood methods.
10. Evolution of bacteriophages: bacteriophage genomes; comparative genomics and genome mosaicism; when the phenetic classification breakes down; classical and new phage evolutionary models.
11. Gene duplication and exon shuffling: types of gene duplication; domains and exons; formation of gene families and the acquisition of new functions; evolution of globin genes and Hox genes.
12. Evolution by transposition: transposition and retroposition; transposable elements; retroelements, retrosequences. Genetic and evolutionary effects of transposition; horizontal gene transfer.
13. Genome evolution: the evolution of genome size in prokaryotes, the minimal genome. Evolution of genome size in eukaryotes.
14. The role of noncoding DNA: repetitive sequences; the possible functions of noncoding DNA. Evolution of noncoding sequences.
Bastien D. Gomperts, Ijsbrand M. Kramer, Peter E.R. Tatham: Signal Transduction, 2nd ed., Academic Press, 2009
Michael Friedman, Brett Friedman: Cell Communication, The Rosen Publishing Group, 2005