Assignments

Special software is required to use some of the files in this section: .py, .pdb (Protein Data Bank), and .zip.


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.)