align.py is the alignment without affine gap
affine_align.py is the alignment without affine gap
These are python 3.5 language.
To run align.py python3 align.py input_file_name
To run affine_align.py python3 affine_align.py input_file_name gap_open_penalty gap_extend_penalty
The penalties are absolute value.
Matrix.txt file must be in the same directory. The code read the blosum62 from it. #