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BIOL478-PP2-Extra-Credit--Hailey-Szadowski/HOWTOUSEPP2.txt

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HOW TO USE PP2.py:
You must have Python modules Bio and NumPy installed.
You must have BLOSUM62 text file, pro1.fasta, and pro2.fasta in the same directory as the program before running.
Only use BLOSUM62 score matrix provided. This is essential as I removed the comments at the top of the NIH-provided BLOSUM62 file.
With current program, you must use a protein sequence named pro1.fasta and DNA sequence and pro2.fasta. These names can be changed by editing lines 9 and 12 of the program.
I have provided pro1.fasta and pro2.fasta containing the sequences used for Example 1 within the Test Cases section of provided report.
To change the maximum number of sub-optimal, non-intersecting alignments, edit line 19 of the program (variable numseq).