The files include:

Project outline: CS5393 - Final Project.pdf

Code: stephen_belcher_R11676566_final_project.py

Scoring matrix: BLOSUM62.mtx

Input file: SequenceData.fna

Intermediate files: sequences.sorted.fna sequences.clustered.fna sequences.nonchimeric.fna sequences.chimeric.fna

Final output file: sequences.msa.fna

TO RUN THE CODE, IN THE TERMINAL ENTER THE FOLLOWING:

python stephen_belcher_R11676566_final_project.py -i SequenceData.fna -o sequences -s BLOSUM62.mtx