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.gitignore
Makefile
McCaskill.cpp
McCaskill.h
README
RNAbor.cpp
RNAbor.h
RNAbor.man
RNAhairpin.h
TODO.txt
batch_runner.rb
batch_runner_in_r.rb
benchmarker.rb
benchmarker_with_mfe.rb
benchmarking.sql
config.h
convert_Vienna.cpp
convert_Vienna.h
divergence.rb
driver.rb
energy_const.h
energy_par.cpp
energy_par.h
fold.cpp
fold.h
fold_vars.cpp
fold_vars.h
intloops.h
misc.cpp
misc.h
myConst.h
pair_mat.cpp
pair_mat.h
params.cpp
params.h
runner.rb
solo_run_in_r.rb
utils.cpp
utils.h

README

This program calculates the number of secondary structures, Boltzman probabilities and partition function of an RNA sequence with respect to the hairpin number K. No dangles. Allow lonely base pairs.
INSTALLATION NOTES
1. type "make"
2. type "make clean"
3. (optional) type "make install", this step will copy the executable "RNAhairpin" into /usr/local/bin, and the man file into /usr/local/man/man1/. If you don't have permission, or your directory system is different from specified above, please do this step manually
4. the executable is "RNAhairpin"