Cray User Group Directory of User-submitted Software

Title NWGAP
Revision 2.0
Purpose Global sequence alignment
Package type Program
Application area Biomedical, Sequence alignment
Abstract NWGAP is a global sequence alignment program. NWGAP uses a modified version of the Needleman and Wunsch algorithm. The most signficant modification is that affine gap penalities can be used. Other modifications include user-defined reduced "set" alphabets. A variety of alignment methods can be selected, including match/mismatch, dayhoff pam-250, structure genetics, properties, and user-defined methods. NWGAP can be used to produce global alignments between two nucleic acid sequences, or two protein sequences.
Submittor Alex Ropelewski
Contact Alex Ropelewski
Phone 412-268-4960
Email ropelewski@psc.edu
Company/
Institution
Pittsburgh Supercomputing Center
4400 Fifth Avenue
Pittsburgh, PA, 15213
CUG Site Code PSC
Distribution method contact the following person: Alex Ropelewski
URL
Distribution restrictions none
Copyright Copyright by PSC, with a free license to users to make a local copy. No redistribution is allowed.
License required no
License fee n.a.
Hardware
Operating System UNICOS 6.0
Compiler(s) CFT77 and C
Program support When schedule permits
Documentation README file, User Manual, test data
Portability to other UNIX systems Program is mixed FORTRAN and C. There will naturally be some porting problems.
Additional comments NWGAP uses the linear space version of the dynamic programming algorithm of Miller and Myers.

Back to the CUGDUS home page
Copyright © 1998 by Cray User Group Inc. All rights reserved.
Last update: April 28, 1998