NESW version 0.1
2010/02/20

usage:

1. Make the source code
   ex: make
2. Generate our original format database file.
   ex: ./bin/convert -g 2 database.fasta dst
3. Execute the smith-waterman algorithm
   ex: ./bin/sw -g 2 matrix/BLOSUM50 qseq.fasta dst.kfasta dst.id

You can get other scoring matrices from ftp://ftp.ncbi.nih.gov/blast/matrices/


