NTDPAL(1)						       Primer3 User Manuals							 NTDPAL(1)

NAME

       ntdpal - Provides Primer3's alignment functionality

SYNOPSIS

       ntdpal [-g gval] [-l lval] [-m mval] [-f1, f2, f3] [-p] [-s] [-e] {seq1} {seq2} {mode}

DESCRIPTION

       Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand-alone program that provides Primer3's alignment functionality (local, a.k.a.
       Smith-Waterman, global, a.k.a. Needleman-Wunsch, plus "half global").

OPTIONS

       -g gval
	   gval is a (positive) float (.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the
	   output score)

       -l val
	   lval is a (positive) float (.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from
	   the output score)

       -a
	   Causes the scoring matrix to be modified by dpal_set_ambiguity_codes.

       -e
	   Causes the end postion of the alignment in both sequences to be printed. Do not confuse with the 'e' mode.

       -f1, -f2, -f3
	   Force specific implementations. -f2 forces use an implementation that might provide more informative error messages, possibly at the
	   expense of some speed.

       -h
	   Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = -0.5. (The default scoring matrix assigns 1 to a
	   match, and -1 to a mismatch.)

       -p
	   Causes the alignment to be displayed on stderr.

       -s
	   causes only the score to printed.

       -m mval
	   is the maximum allowed gap (default is 3).

       seq1 and seq2
	   are the sequences to be aligned.

       mode
	   is one of g, G, l, or L specifying a global, global end-anchored, local, or local end-achored alignment respectively. For backward
	   compatibility e is equivalent to G.

REFERENCE

       Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener,
       eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.

SEE ALSO

       primer3_core(1) oligotm(1)

COPYRIGHT

       Copyright (C) 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen
       (http://jura.wi.mit.edu/rozen), Helen Skaletsky

       All rights reserved. On Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the licence of ntdpal.

       This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is
       granted to copy, distribute and/or modify this document under the same terms as oligotm itself.

ntdpal 1.1.4							    05/09/2008								 NTDPAL(1)