ct-prob — calculate probabilities based on a .ct file.


ct-prob [OPTION]... FILE.ct [FILE.plot]


ct-prob reads a set of stuctures in .ct format from FILE.ct and computes the probability of each base pair. These probabilities are written to standard output, in the same format as the .plot files written by hybrid, hybrid-ss, etc.

If FILE.plot is given, it is taken to contain the expected probabilities for each base pair. The output is then extended to include for each base pair the expected probability, the standard deviation and the relative error.


-w, --weighted
compute a weighted average, where the weights are the Boltzmann factors for each structure. Each Boltzmann factor is computed from a header line in the .ct file.
-t, --temperature=REAL
set the temperature for Boltzmann-weighting to REAL °C. Default is 37.
-s, --single
output single-strandedness probabilities in .ext format instead of base pair probabilities.


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), hybrid-intra(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