| ASSIGNMENTS | SUPPORTING FILES |
|---|---|
| Module 1: Phylogenetic Inference | |
| Assignment 1 (PDF) | hw1_files.zip (ZIP - 1.1 MB) (This zip file contains: solutions to fibonacci and UPGMA portions.) |
| Assignment 2 (PDF) | hw2_files.zip (ZIP) (This zip file contains: codebase (hw2.py), example tree (hw2_tree.txt), and a solution (hw2_sol.py).) |
| Assignment 3 (PDF) | hw3_files.zip (ZIP) (This zip file contains: codebase (hw3.py); example trees in Newick form (hw3_tree.txt) and diagram (hw3_tree.pdf); a helper smaller test tree with answers (hw3_helper.pdf); and solution (hw3_sol.py).) |
| Assignment 4 (PDF) | hw4_files.zip (ZIP) (This zip file contains: codebase (hw4.py); example tree (hw4_tree.txt) and sequence alignment (hw4_seqs.aln); and solution (hw4_soln.py).) |
| Assignment 5 (PDF) | hw5_files.zip (ZIP) (This zip file contains: codebase (hw5.py); example tree (hw5_tree.txt) and sequence alignment (hw5_seqs.aln); jukes-cantor placeholding code (hw5_evomodel_sad.pdf); a solution (hw5_sol.py); and a derivation (hw5_derivation.pdf).) |
| Module 2: Molecular Modeling | |
| Assignment 6 (PDF) | hw6_files.zip (ZIP) (This zip file contains: example data (hw6_data.txt) and syntax helper (hw6_helper.pdf).) |
| Assignment 7 (PDF) | hw7_files.zip (ZIP) (This zip file contains: example data (hw7_data.txt); Python® module for vector math (vector.py); and a solution (hw7_sol.txt).) |
| Assignment 8 (PDF) | hw8_files.zip (ZIP) (This zip file contains: code and data files.) |
| Assignment 9 (PDF) | hw9_files.zip (ZIP) (This zip file contains: code and data files.) |
| Module 3: Discrete Reaction Events | |
| Assignment 10 (PDF) | hw10_files.zip (ZIP) (This zip file contains: directory of code and data files (\media) and solutions in PDF and Python® form.) |
| Assignment 11 (Optional) (PDF) | hw11_files.zip (ZIP) (This zip file contains: directory of code and data files (\media), hints and solution.) |