FFTbor computes number of delta-neighbours and the partition function of delta-neighbours.
Type FFTbor --help
for help on the input format.
This software depends on the presence of the following programs:
- A valid C++ compiler with OpenMP support (developed using GCC 4.8 but should support any reasonable C++98 compiler)
- CMake (>= 2.6, to generate the Makefile)
- FFTW (= 3.3.x)
libRNA.a
from the ViennaRNA package (= 2.x)
To compile the program using CMake, perform the following commands:
cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
make
make install
- If
libRNA.a
is in a non-standard location, you can specify its path with the-CMAKE_LIBRARY_PATH
flag.- See this list of CMake environment flags for more details.
- The
-DCMAKE_INSTALL_PREFIX
flag is not strictly necessary, and uses/usr/local
as a default. make install
may need administrator privileges, depending on the permissions of your target install prefix.- CMake >= 2.6 is required to generate the system-appropriate Makefile.
- main.c - the main program file, reads input and prints output.
- delta.c, delta.h - the algorithm implementation.
- misc.c, misc.h - a few additional functions and global variables.
- energy_const.h, energy_par.h, params.h - three h-files from ViennaRNA, these define energy parameters.
- rna_turner1999.par, rna_turner2004.par - the energy parameters (in the Vienna 2.x format).
- libRNA.a - Vienna RNA library file, this file is not included in this tar-ball, but is generated by compiling the Vienna RNA package.
- CMakeLists.txt - the CMake manifest for this package.