--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAHEAT "1" "July 2013" "RNAheat 2.1.2" "User Commands"
+.SH NAME
+RNAheat \- manual page for RNAheat 2.1.2
+.SH SYNOPSIS
+.B RNAheat
+[\fIoptions\fR]
+.SH DESCRIPTION
+RNAheat 2.1.2
+.PP
+calculate specific heat of RNAs
+.PP
+Reads RNA sequences from stdin and calculates their specific heat in the
+temperature range t1 to t2, from the partition function by numeric
+differentiation. The result is written to stdout as a list of pairs of
+temperature in C and specific heat in Kcal/(Mol*K).
+The program will continue to read new sequences until a line consisting of the
+single character "@" or an end of file condition is encountered.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Print help and exit
+.TP
+\fB\-\-detailed\-help\fR
+Print help, including all details and hidden
+options, and exit
+.TP
+\fB\-\-full\-help\fR
+Print help, including hidden options, and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print version and exit
+.SS "General Options:"
+.IP
+Below are command line options which alter the general behavior of this
+program
+.TP
+\fB\-\-Tmin\fR=\fIt1\fR
+Lowest temperature
+.IP
+(default=`0')
+.TP
+\fB\-\-Tmax\fR=\fIt2\fR
+Highest temperature
+.IP
+(default=`100')
+.TP
+\fB\-\-stepsize\fR=\fIFLOAT\fR
+Calculate partition function every stepsize
+degrees C
+.IP
+(default=`1.')
+.TP
+\fB\-m\fR, \fB\-\-ipoints\fR=\fIipoints\fR
+The program fits a parabola to 2*ipoints+1 data
+points to calculate 2nd derivatives. Increasing
+this parameter produces a smoother curve
+.IP
+(default=`2')
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide "T"
+with "U"
+.IP
+(default=off)
+.SS "Model Details:"
+.TP
+\fB\-4\fR, \fB\-\-noTetra\fR
+Do not include special tabulated stabilizing
+energies for tri\-, tetra\- and hexaloop hairpins.
+Mostly for testing.
+.IP
+(default=off)
+.TP
+\fB\-d\fR, \fB\-\-dangles\fR=\fIINT\fR
+How to treat "dangling end" energies for bases
+adjacent to helices in free ends and multi\-loops
+.IP
+(default=`2')
+.IP
+With \fB\-d2\fR dangling energies will be added for the bases adjacent to a helix on
+both sides in any case
+.HP
+\fB\-d0\fR ignores dangling ends altogether (mostly for debugging).
+.TP
+\fB\-\-noLP\fR
+Produce structures without lonely pairs (helices
+of length 1).
+.IP
+(default=off)
+.IP
+For partition function folding this only disallows pairs that can only occur
+isolated. Other pairs may still occasionally occur as helices of length 1.
+.TP
+\fB\-\-noGU\fR
+Do not allow GU pairs
+(default=off)
+.TP
+\fB\-\-noClosingGU\fR
+Do not allow GU pairs at the end of helices
+.IP
+(default=off)
+.TP
+\fB\-P\fR, \fB\-\-paramFile\fR=\fIparamfile\fR
+Read energy parameters from paramfile, instead of
+using the default parameter set.
+.IP
+A sample parameter file should accompany your distribution.
+See the RNAlib documentation for details on the file format.
+.TP
+\fB\-\-nsp\fR=\fISTRING\fR
+Allow other pairs in addition to the usual
+AU,GC,and GU pairs.
+.IP
+Its argument is a comma separated list of additionally allowed pairs. If the
+first character is a "\-" then AB will imply that AB and BA are allowed
+pairs.
+e.g. RNAfold \fB\-nsp\fR \fB\-GA\fR will allow GA and AG pairs. Nonstandard pairs are
+given 0 stacking energy.
+.TP
+\fB\-e\fR, \fB\-\-energyModel\fR=\fIINT\fR
+Rarely used option to fold sequences from the
+artificial ABCD... alphabet, where A pairs B,
+C\-D etc. Use the energy parameters for GC (\fB\-e\fR
+1) or AU (\fB\-e\fR 2) pairs.
+.SH AUTHOR
+
+Ivo L Hofacker, Peter F Stadler, Ronny Lorenz
+.SH REFERENCES
+.I If you use this program in your work you might want to cite:
+
+R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011),
+"ViennaRNA Package 2.0",
+Algorithms for Molecular Biology: 6:26
+
+I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994),
+"Fast Folding and Comparison of RNA Secondary Structures",
+Monatshefte f. Chemie: 125, pp 167-188
+
+
+.I The energy parameters are taken from:
+
+D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004),
+"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure",
+Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292
+
+D.H Turner, D.H. Mathews (2009),
+"NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure",
+Nucleic Acids Research: 38, pp 280-282
+.SH "REPORTING BUGS"
+If in doubt our program is right, nature is at fault.
+.br
+Comments should be sent to rna@tbi.univie.ac.at.
+.SH "SEE ALSO"
+
+RNAfold(1)
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