ct-energy — evaluate the energy of a .ct file


ct-energy [OPTION]... [FILE]...


ct-energy evaluates the energy of each structure in each FILE, such as those produced by mfold or by hybrid-min or hybrid-ss-min. In its default mode it prints the energy of each structure followed by a carriage return (but see the --verbose option below).

When no FILE is specified, or if FILE is -, ct-energy reads standard input.


set nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=REAL
set temperature to REAL °C. Default is 37.
-N, --sodium=REAL
set Sodium ion concentration to REAL molar. Default is 1.
-M, --magnesium=REAL
set Magnesium ion concentration to REAL molar. Default is 0.
-p, --polymer
use salt corrections for polymers instead of oligomers (the default).
-s, --suffix=STRING
use energy rules with the suffix STRING. Overrides --temperature, --sodium, --magnesium and --polymer.
-v, --verbose
output detailed information about each loop in the structure. Specify twice for even more verbosity.
-L, --logarithmic
make the penalty for multibranch loops logarithmic rather than linear.


remove single-base stacking from consideration.
make the penalty for multibranch loops constant rather than affine.
consider single-base stacking in "Vienna mode", in which a single-stranded base that may stack on an adjacent basepair must always do so. By default, two states are considered for each such base: dangling and not dangling.
consider coaxial stacking.


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. ct-energy 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-min(1), hybrid-ss-min(1)


Nick Markham <> and Michael Zuker <>


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


UNAFold is available from Commercial use requires a license; see