[Bioperl-l] Added Phil Green's Smith-Waterman to my module

[Yee Man]

Hi, Aaron,

	After some hacking, I added the code in dropgsw.c in the FASTA
release to my DNA Smith-Waterman module. You can download it and try it
out at http://www.stanford.edu/~yeeman/dsw.tgz. There are two files called
t1.fa, t2.fa for your testing.

	This implementation doesn't do frame shift or reverse complement,
it is just a plain alignment.

	I also discovered that the performance result I reported
for FASTA's Phil Green didn't say that you have to use the cc compiler and
the compiler options in the makefile. If I use gcc and then only use -g
option, it finishes alignment with t1.fa, t2.fa with -3 option will go
from 6sec to 12sec. My vanilla implementation of SW gives us about 50sec
with gcc and -g option.

Regards,
Yee Man