---
name: "ntdpal"
section: "1"
platform: "linux"
package: "primer3"
version: "2.6.1-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ntdpal"
---

# ntdpal(1)

Provides Primer3's alignment functionality

## 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)](/primer3_core/1.md) [**oligotm**(1)](/oligotm/1.md)

## 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.