alignment

Alignment of genomic sequences using the Needleman-Wunsch algorithm (global alignment) or the Smith-Waterman algorithm (local alignment).

How to build and run?

To build: Just call make

For a global DNA alignment:

./Alignment TACTACCAGA TACTAGGGGG

For a global RNA alignment:

./Alignment UACUAGCCAGA UACUAGGGG

For a local alignment: ./Alignment -l TAC AAAAAAAAAAGGGTACTTTT