NAME — create an isothermal titration calorimetry plot


DESCRIPTION simulates isothermal titration calorimetry (ITC), in which the concentration of one sequence is held constant while that of the other sequence is slowly increased. An ITC plot shows the enthalpy change at each step divided by the change in concentration as a function of concentration.

hybrid and hybrid-ss, or their equivalents, must be run for the five species before running This is most easily done with


set nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=REAL
set temperature to REAL °C. Default is 37.
-A, --A0=REAL
fix the total concentration of A present at REAL molar.
-B, --B0=REAL
fix the total concentration of B present at REAL molar.
-x, --exclude=A|B|AA|BB
exclude the specified species from consideration. May be used more than once, to exclude multiple species.
assign the fraction REAL of the stacking enthalpy for each sequence with its reverse complement to stacking in the single strands. Default is 0.1. To disable entirely, use --nofraction.
remove stacking in unfolded single strands from consideration.
assign entropy to single strands so that melting temperature is REAL °C. Default is 50.
-o, --output=prefix
name output files with prefix.
-r, --reuse
assume that has already been run and create a new plot based on existing ITC data.
create hyperbolic plots (enthalpy versus concentration) instead of sigmoidal plots (change in enthalpy divided by change in concentration versus concentration).


an alternate location from which to read the energy rules. The default energy rules can be overridden with files in the current directory or in the directory pointed to by UNAFOLDDAT. looks for each file first in the current directory, then in the directory specified by UNAFOLDDAT and last in /usr/local/share/unafold (or wherever the energy rules were installed).


Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.

Other references which may be useful may be found at


hybrid(1), hybrid-ss(1),


Nick Markham <> and Michael Zuker <>


Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.


Both commercial and non-commercial use of UNAFold require a license from RPI; see