NAME — create a van't Hoff plot.


DESCRIPTION creates a van't Hoff plot, in which the inverse of melting temperature is plotted as a function of the logarithm of total strand concentration. For a two-state melt, this results in a line with slope equal to R divided by the enthalpy change.

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.
-C, --Ct=REAL
set total strand concentration to 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.


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.


UNAFold is available from Commercial use requires a license; see