| Topic |
Date |
Remarks |
| Introduction |
01/17/07 |
Slides |
| Perl |
01/19/07 |
Slides Basic Unix commands |
| Alignment |
01/24/07 |
Animation
for alignment dynamic programming algorithm |
| Alignment in Perl |
01/26/07 |
|
| Alignment |
01/31/07 |
|
| Alignment in Perl |
02/2/07 |
HW 1 |
| Alignment heuristics |
02/7/07 |
Slides |
| Alignment in Perl |
02/9/07 |
|
| Class cancelled |
02/14/07 |
|
| Alignment in Perl |
02/16/07 |
BLOSUM 62 matrix PREFAB pairwise alignments |
| Comparing two alignments |
02/21/07 |
|
| Comparing two alignments in Perl |
02/23/07 |
HW 2 |
| Comparing two alignments in Perl |
02/28/07 |
|
| Training protein pairwise alignment on PREFAB |
03/02/07 |
|
| Distance-based phylogeny reconstruction |
03/07/07 |
|
| Training pairwise alignment on PREFAB | 03/09/07 |
HW 3 Program to score an alignment |
| Spring break | 03/14/07 |
|
| Spring break | 03/16/07 |
|
| Distance-based phylogeny reconstruction | 03/21/07 |
Slides |
| Alignment | 03/23/07 |
Optimal pairwise alignment program in Perl Gap training Scoring alignments: Upper case residues only |
| Phylogeny reconstruction (distance based) | 03/28/07 |
Slides |
| Alignment | 03/30/07 |
HW 4 SIMPLE substitution matrix Training and testing datasets |
| Distance based phylogeny reconstruction | 04/04/07 |
|
| Training alignment parameters | 04/06/07 |
|
| UPGMA in Perl | 04/11/07 |
|
| UPGMA in Perl | 04/13/07 |
|
| NJ | 04/18/07 |
|
| UPGMA in Perl in newick format | 04/20/07 |
HW 5 |
| NJ and UPGMA with branch lengths | 04/25/07 |
|
| Review | 04/27/07 |
UPGMA in Perl |
| Final exam | 05/02/07 |