ensemble-ext, ensemble-ext-same — compute extinction of an ensemble of species


ensemble-ext [OPTION]... PREFIX1 ensemble-ext-same [OPTION]... PREFIX


ensemble-ext computes the extinction of a two-sequence ensemble. The input to ensemble-ext consists of the outputs of running hybrid or hybrid-ss on each species, as well as the output of running concentration on the ensemble. ensemble-ext writes PREFIX1-PREFIX2.ens.ext which containts the extinction of the ensemble at each temperature. It also writes PREFIX1-PREFIX2.ens.TmExt1 and PREFIX1-PREFIX2.ens.TmExt2, which contain the inflection and halfway points of the extinction curve. Both are approximations of the melting temperature; the latter is preferred. The file PREFIX1-PREFIX2.ens.MaxExt contains the maximum possible extinction, i.e. the extinction if all bases were unpaired.

ensemble-ext-same operates in the same manner on a one-sequence ensemble, using the output from concentration-same.

It is recommended to use to run hybrid, hybrid-ss, concentration,, ensemble-dg and ensemble-ext instead of running ensemble-ext directly.


set nucleic acid type to RNA or DNA. Default is RNA.
-p, --points=NUMBER
use NUMBER points on either side of each point when performing numerical differentiation to determine the inflection point. Default is 1.
-x, --exclude=A|B|AA|BB
exclude the specified species from consideration. May be used more than once, to exclude multiple species.
-o, --output=STRING
name output files with the prefix STRING.


only sum extinctions for each nucelotide, rather than for each dinucleotide.


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), concentration(1), concentration-same(1),


Nick Markham <> and Michael Zuker <>


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Both commercial and non-commercial use of UNAFold require a license from RPI; see