I'm writing a Python program and I have to do a pairwise alignment on several thousand DNA sequences. I looked at Biopython but I couldn't fine a function to do a pairwise alignment, this may be my mistake. The function should have gap penalty, gap open, gap extension and Smith Waterman or Needleman Wunsch. Can anyone tell me where I can find a good Python package for doing this kind of alignment?
thanks in advance