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Refresh MBI4750 lecture slides

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  1. intro, pathogen discovery
  2. genetic distances, clustering for nomenclature
  3. clustering for epidemiology
  4. clustering for tree building (neighbor-joining)
  5. substitution models (Markov chains)
  6. maximum likelihood, ML trees
  7. dN/dS
  8. model selection, likelihood ratio test, AIC
  9. rooting trees
  10. molecular clocks, root-to-tip regression
  11. Bayesian inference
  12. MCMC
  13. Coalescent (after reading week)
  14. Demographic models. Skylines
  15. BEAST.
  16. Modeling epidemics. Comparmental models.
  17. Birth-death models.
  18. Birth-death models (part 2)
  19. Guest lecture (Abayomi)
  20. Phylogeography (Devin)
  21. Ethics of data sharing (privacy, open access)
  22. Ethics of sharing tools (open source)
  23. Guest lecture (Roux-Cil)
  24. Guest lecture (Jeff)