[Bioperl-l] RE: FASTA Smith-Waterman (Swat) implementation

William R. Pearson wrp at alpha0.bioch.virginia.edu
Mon Jan 27 10:15:23 EST 2003


There are no licensing issues (that I know of) in using Phil Green's
SWAT optimization in Smith-Waterman implementations.  I am not
actually using his code; I am using his insight.

Although the FASTA package is copyrighted, some of the code that I
mostly got from other people, such as the Smith-Waterman
implementation and linear space alignment code (from Webb Miller), I
have offered to other open source projects (EMBOSS) and I am happy to
have BioPerl use the code as well.

Some of Webb Miller's code for these things is available from:
http://globin.cse.psu.edu/ftp/dist/sim/
I believe that Webb has placed this code in the public domain.

Bill Pearson



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