Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization.  In Keith, J. M., editor, \fIBioinformatics, Volume II.  Structure, Functions and Applications\fR, number 453 in \fIMethods in Molecular Biology\fR, chapter 1, pages 3-31.  Humana Press, Totowa, NJ.  ISBN 978-1-60327-428-9.
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Other references which may be useful may be found at http://dinamelt.bioinfo.rpi.edu/refs.php.
