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

# ntthal(1)

Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach

## NAME

ntthal - Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach

## DESCRIPTION

**ntthal** is analogous to **ntdpal**.  Between two sequences, **ntthal** finds alignment/sec structure, that has the highest melting temperature. Ntthal is based on nearest-neighbor thermodynamical approach.

## SYNOPSIS

**ntthal** *OPTIONS* oligo

## OPTIONS

**-mv** monovalent\_conc  - concentration of monovalent cations in mM, by default 50 mM

**-dv** divalent\_conc    - concentration of divalent cations in mM, by default 0 mM

**-n**  dNTP\_conc        - concentration of deoxynycleotide triphosphate in mM, by default 0 mM

**-d**  dna\_conc         - concentration of DNA strands in nM, by default 50 nM

**-a**  mode             - alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)

**-t**  temp             - temperature at which duplex is calculated, by default 37C

**-r**                   - causes the alignment NOT to be displayed on stderr, \_only\_ Tm is printed

**-maxloop** size        - the maximum size of secondary structures loops.

-

  Default is 30 (this is maximum allowed length, currently).

**-path** \<path\>         - the path to the thermodynamic parameter files

**-s1** DNA\_oligomer

**-s2** DNA\_oligomer

## AUTHORS

This manual page was created by Andreas Tille \<tille@debian.org\> using help2man for Debian but can be freely used for any other purpose