1. Exercise Med11 Topics: homology = orthology, phylogenetic profile, distant homology, PFAM, BLAST, PSI-BLAST, CLUSTAL, HMMER, PHMMER.
  2. Exercise BEM2 Topics: domains, domain topology, SMART. PFAM, CDD, key genomes.
  3. Exercise ARHGAP29 Topics: BLAST, ENSEMBL, NR, Gene family evolution
  4. Exercise NUDIX Topics: clustal, neighbor-joining, iToL, tree of domains, internal duplications
  5. Exercise RasGEF Topics: orthology, paralogy, gene loss, phylogenetic tree, tree reconciliation,
  6. Optional Exercise PLK1 Topics: clustal, neighbor-joining, blast/phmmer,duplications
  7. Exercise RPL22 Topics: endosymbiosis, tree reconciliation, nuclear transfer, tree of life.
  8. Exercise MSC1 Topics: clustal, neighbor-joining, blast/phmmer,duplications
  9. Exercises WGD
  10. Exercise peroxisome Topics: gene duplication, eukaryogenesis, tree reconciliation, protein re-location.
  11. Exercises Genome and Module Evolution in terms of Gene Content.