ct2rnaml — convert .ct file to RNAML


ct2rnaml prefix


ct2rnaml reads prefix.ct and converts it to prefix.rnaml. All sequences and structures are encoded in the RNAML file; in addition, initial and/or revised energies are included if they are found in the .ct file.

ct2rnaml also reads the coordinatse of each base pair from or (where # is the number of the structure).


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

Waugh, A. et al. (2002) RNAML: a standard syntax for exchanging RNA information. RNA, 8(6), 707-717.


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