20.181:Assignments

Phylogenetic Inference

1. Assignment #1 PDF due before Sept. 14 (due on Wednesday before midnight)
   • solution to fibonacci portion
   • solution to UPGMA portion
2. Assignment #2 PDF due before Sept. 19
   • hw2.py: codebase for assignment #2 (run with "python hw2.py")
   • Example tree
   • a solution
3. Assignment #3 PDF due before Sept. 21,
   • Hw3.py: codebase for assignment #3 run with "python hw3.py",
   • Example tree in Newick form
   • pdf of example tree
   • smaller test tree (with answers)
   • a solution
4. Assignment #4 PDF due before Sept. 28
   • hw4.py codebase for hw4
   • Example tree
   • Example sequence alignment
   • Using sets in Python
   • a solution
5. Assignment #5 PDF due before Oct. 10
   • hw5.py codebase for hw5 updated! -Sonia 19:58, 5 October 2006 (EDT)
   • Example tree
   • Example sequence alignment
   • jukes-cantor placeholding code
   • a solution
   • a derivation

Molecular Modeling

1. Assignment #6 PDF due before Oct. 17
   • Example data
   • HW6 Syntax Helper
2. Assignment #7 PDF due before Oct. 27
   • Example data
   • Python module for vector math
   • the answers!
3. Assignment #8 PDF due before Nov. 7
   • Code and data for hw8
4. Assignment #9 PDF due before Nov. 15
   • Code and data for hw9
   • help with getting the codebase onto your athena account

Discrete Reaction Events

1. Assignment #10 PDF due by midnight on December 4th
   • Media:Hw10.zip
   • File:Athena help2.txt