Special software is required to use some of the files in this section: .py, .pdb (Protein Data Bank), and .zip.
Assignments table.
| 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).)
Using Sets in Python®
|
| 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.) |