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 penalty for creating a gap
           respectively (the penalties are subtracted from the output score)

       -l val
           lval is a (positive) float (.01 precision) specifying penalty 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 position 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-anchored 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 © 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.