[Bioperl-l] Source code for SW algorithm?

[Aaron J Mackey]

the fasta distribution (ftp.virginia.edu/fasta/) includes "ssearch", which
(in addition to SWAT) provides the "definitive" smith-waterman algorithm,
including Hirschberg divide-and-conquer (i.e. Myers & Miller
linear-space), Gotoh's affine gap penalties and various statistical models
under which to test your hits for significance.

The "dropgsw.c" file contains the "standard" smith-waterman code,
including Phil Green's optimization.  "dropnsw.c" is identical but lacks
the Phil Green optimization.

-Aaron

On Fri, 6 Apr 2001, Simon Lin wrote:

> Is the source code (in C?) of the Smith-Waterman algorithm available
> somewhere?
>
> Thanks!
>
> Simon
>
>
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