stretcher calculates a global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space.

Here is a sample session with stretcher:

% stretcher tsw:hba_human tsw:hbb_human
Finds the best global alignment between two sequences
Output alignment [hba_human.stretcher]:

Mandatory qualifiers:

[-sequencea] (sequence)

Sequence USA.

[-sequenceb] (sequence)

Sequence USA.

[-outfile] (align)

Output alignment filename.

Optional qualifiers:

-datafile (matrix)

This is the scoring matrix file used when comparing sequences. By default, it is the file EBLOSUM62 (for proteins) or the file EDNAFULL (for nucleic sequences). These files are found in the data directory of the EMBOSS installation.

-gappenalty (integer)

Gap penalty.

-gaplength (integer)

Gap length penalty.