Homework 3 for CSCE 471/871 (Spring 2013)

Assigned Tuesday, March 26
Due Sunday, April 21 Wednesday, April 24 at 11:59 p.m. Total points: 100

When you hand in your results from this homework, you should submit the following, in separate files:

1. A single .zip file called username.zip where username is your username on cse. In this zip file, put:
   • Source code in the language of your choice (in plain text files).
   • A makefile and a README file facilitating compilation and running of your code (include a description of command line options). If I cannot easily re-create your experiments, you might not get full credit.
   • All your data and results (in plain text files), except for data provided to you.
2. A single .pdf file with your writeup of the results for all the homework problems, including the last problem. Only pdf will be accepted, and you should only submit one pdf file, with the name username.pdf, where username is your username on cse. Include all your plots in this file, as well as a detailed summary of your experimental setup, results, and conclusions. If you have several plots, you might put a few example ones in the main text and defer the rest to an appendix. Remember that the quality of your writeup strongly affects your grade. See the web page on "Tips on Presenting Technical Material".

Submit everything by the due date and time using the web-based handin program.

On this homework, you must work on your own and submit your own results written in your own words.

1. (100 pts) Implement the Neighbor Joining algorithm for building phylogenetic trees. Choose a reasonable distance measure for your algorithm, and justify your choice in your report. Then build a tree based on this data set and output the tree in Newick format.
   
   In your report, discuss your choice of distance function and how effective you think it was. Also, include in your report a graphical image of the tree, rendered by any program you wish. Finally, include in your .zip file a text file with your Newick-based tree description.

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Last modified 18 April 2013; please report problems to sscott AT cse.