1. Exercise gene trees basics from the introduction to bioinformatics master course Topics: iToL, rerooting, SARS, histons, clustal, looking at the alignment.
  2. Exercise gene trees duplications from the introduction to bioinformatics master course Topics: iToL, clustal, ENSEMBL compara, blast, annotating a gene tree, duplications, reconstructing gene family dynamics, PFKFB4
  3. Exercise PLK1 Topics: clustal, neighbor-joining, blast/phmmer, timing of duplications
  4. Exercise RasGEF Topics: orthology, paralogy, gene loss, phylogenetic tree, tree reconciliation,
  5. Exercise Med11 Topics: homology = orthology, phylogenetic profile, distant homology, PFAM, BLAST, PSI-BLAST, CLUSTAL, HMMER, PHMMER.
  6. Exercise BEM2 Topics: domains, domain topology, SMART. PFAM, CDD, key genomes.
  7. Exercise NUDIX Topics: clustal, neighbor-joining, iToL, tree of domains, internal duplications
  8. Exercise RPL22 Topics: endosymbiosis, tree reconciliation, nuclear transfer, tree of life.
  9. Exercise peroxisome Topics: gene duplication, eukaryogenesis, tree reconciliation, protein re-location.
  10. Exercises WGD
  11. Exercise MSC1 Topics: clustal, neighbor-joining, blast/phmmer,duplications
  12. OPTIONAL Exercise ARHGAP29 Topics: BLAST, ENSEMBL, NR, Gene family evolution
  13. Exercises Genome and Module Evolution in terms of Gene Content.