Needleman-Wunsch global sequence alignment
[EDIT 01-01-2010] this is now available at bitbucket . I've written a simple, fast, python version of Needleman-Wunsch as I couldn't find one to use. It uses Cython and specifically cython-numpy goodness. It's easy-installable as: sudo easy_install -UZ http://bpbio.googlecode.com/svn/trunk/nwalign/ or via svn from: svn co http://bpbio.googlecode.com/svn/trunk/nwalign/ it will put an executable 'nwalign' into /usr/bin/ which when run will give this message: Usage: nwalign [options] seq1 seq2 Options: -h, --help show this help message and exit --gap=GAP gap extend penalty (must be integer <= 0) --gap_init=GAP_INIT gap start penalty (must be integer <= 0) --match=MATCH match score (must be integer > 0) --mismatch=MISMATCH gap penalty (must be integer < 0) --matrix=MATRIX scoring matrix in ncbi/data/ format, if not specificied, match/mismatch are used where the matrix is optional