Models and Simulations in Molecular Evolution

Instructor:

Readings:

  1. Week 1: Chapter 1 from Durbin, R, S Eddy, A Krogh, and G Mitchison. 1998. Biological Sequence Analysis Cambridge University Press
  2. Week 2: Posada, D and KA Crandall. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology 50:580-601.
  3. Week 3: Goldman, N, JP Anderson, and AG Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49:652-70.
  4. Week 4: No reading.
  5. Week 5: Sanderson, MJ. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218-31.
  6. Week 5: Aris-Brosou, S and Z Yang. 2003. Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Molecular Biology and Evolution in press.
  7. Week 7: Yang, Z and R Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19:908-917.
  8. Week 7: Dias, AP, EL Braun, MD McMullen, and E Grotewold. 2003. Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after fuplication. Plant Physiology 131:610-620.
  9. Week 8: Hughes, AL. 2002. Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues. J Mol Evol 54:90-101.
  10. Week 8: optional reading - Pupko, T, Sharan, R, Hasegawa, M, Shamir, R, and Graur, D 2001. A chemical-distance-based test for positive Darwinian selection. Proceeding of the 1st Workshop on Algorithms in BioInformatics BRICS, University of Aarhus, Denmark, August 28-31, 2001.
  11. Week 9: Eddy, SR. 1998. Profile hidden Markov models. Bioinformatics 14:755-63.
  12. Week 9: Collins, LJ, AM Poole and D Penny. 2003. Using ancestral sequences to uncover potential gene homologs. Applied Bioinformatics in press.
  13. - Download the text, figures, supplementary figures, and supplementary tables for Collins et al. in press.

Notes:

  1. Powerpoint notes for Week 1.
  2. Powerpoint notes for Week 2.
  3. Powerpoint notes for Week 3.
  4. Powerpoint notes for Week 4.
  5. Powerpoint notes for Week 5.
  6. Powerpoint notes for Week 7.
  7. Powerpoint notes for Week 9.

Additional Info:

  1. Guidelines for the paper.
  2. An excel spreadsheet with word documentation to help you learn likelihood calculations.
  3. A list of programs you may find useful (for week 4).