I wrote:         
  >>> nwalign.global_align("PLEASANTLY", "MEANLY", gap_open=-5, gap_extend=-5, 
matrix='./BLOSUM62.txt')
  >>> ('PLEASANTLY', '-MEA--N-LY')

I forgot to mention that I got my BLOSUM62.txt from
  http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt

in case that matters.

Laura
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