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