Written originally for aligning proteing sequences.  Don't have a makefile yet, just need a simple one to compile main.c.

Run as: align sequences_filename substitution_matrix_filename gap_init_penalty gap_ext_penalty

This is a modified form of the Needleman-Wunsch algorithm that uses affine gap scores which basically means instead of penalizing
gaps the same way at each position, the penalty decreases as you add more gaps to an existing gap.  The analogy being if an
organism mutated and removed a section from a protein, it's not linearly less likely for a larger section to be removed than a smaller one.

TODO:
Change to RNA, which basically means changing the substitution matrix file to be 4x4
Make sure nothing is hardcoded in their looking for 20 amino acids (though I think I programmed it generally)
Pull new RNA sequences to align
Study the affine gap stuff so we're able to explain ourselves (I can probably do that)
Implement a non-dynamic programming algorithm to do part 2 of the project
(Optional) Do multi-sequence alignment, I've got a book from bioinformatics and you basically just make an n-dimensional matrix instead of 2