Smith-Waterman-Eggert including multiple subsequence alignment

[Martijn Huynen]

Hi

Does anybody have C-code for the modified version of the Smith-Waterman
algorithm that also gives "non-intersecting similar subsequences" 
(published in J. Mol. Biol. (1987) 197, 723-728 by Waterman and Eggert)
(the disadvantage of the original Smith-Waterman code is that it only
gives one "hit" per pair of sequences, Blast does not have this disadvantage
but is less rigorous/sensitive)

many thanks, Martijn

Martijn Huynen
Biocomputing Group, EMBL
Meyerhofstrasse 1
69012  Heidelberg, Germany
tel: +49-6221-387372
fax: +49-6221-387517