| WEEK | DATE | LAB TOPIC | ASSIGNMENT |
| 1 | Aug 24 | Building a first tree (BOLD/MEGA/FigTree) | Exercise 1  |
| 2 | Aug 31 | Phylogeny and a murder trial (Metzker et al.) and Online genomic resources (NCBI Assignment presentations) |
Exercise 2  |
| 3 | Sep 7 | Mitochondrial (mt) genes across mollusks and selected outgroups | Exercise 3  |
| 4 | Sep 14 | Multiple sequence alignment/Tree Building Methods (PTME Chs. 4 & 5; PAUP*) See Thompson et al. 1994 (TITANium) - Edgar 2004 (MUSCLE) - Larkin et al. 2007 (CLUSTALW2) - Goujon et al. 2010 (EMBL-EBI) |
Exercise 4  |
| 5 | Sep 21 | Multiple sequence alignment/Tree Building Methods (cont.) | Exercise 4 |
| 6 | Sep 28 | Simulation of sequence evolution (Li pp. 1-11, 21-34, skim 12-20) | Exercise 5 |
| 7 | Oct 5 | Maximum Likelihood/Bayesian Inference (PTME Chs. 9 & 10) | Exercise 6 |
| 8 | Oct 12 | PCR and primer design (Reading TBA) | Exercise 7  |
| 9 | Oct 19 | PCR and primer design (Class Project) | Exercise 7 (cont.) |
| 10 | Oct 26 | PCR and primer design (Class Project) | Exercise 7 (cont.) |
| 11 | Nov 2 | Applying phylogenetic methods (Start Final Project) | Exercise 8  |
| 12 | Nov 9 | Assembling sequence contigs | Exercise 9  |
| 13 | Nov 16 | Work on Final Project | |
| 14 | Nov 21-25 | Fall Break | No Class |
| 15 | Nov 30 | Work on Final Project | No handouts |
| 16 | Dec 7 | Final Presentations | TBA |
| Final | Dec 12 | FINAL PROJECTS DUE (No Exam) | 5 PM - MH282 |