This project will include a solid implementation of the Max of Pairs sequence alignment algorithm in Python as the eventual goal. The code might be eventually ported to Java or C++ for speed concerns, but NumPy is an excellent array programming environment.

Currently this code includes various parts in different states:

• Needleman Wunsch implementation
• Max of Pairs implementation
• Sum of Pairs implementation
• Visualization (with PIL)
• FASTA reading