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