RNAStructProfiling

Compiler dependencies: To compile and install RNAStructProfiling, you will need
--a C/C++ compiler
--autotools
--GMP (version 6.0.0 from gmplib.org)
Parallelization requirements: For parallelization, the compiler needs to implement the OpenMP API.
(GNU gcc 4.7, for example, implements the OpenMP API. See http://openmp.org/wp/openmp-compilers for details.)

To download source code, click on "zip" link on the RNAStructProfiling github
page (https://github.com/gtfold/RNAStructProfiling/zipball/master).

To compile on a Mac OSX machine, make sure your dependencies are satisfied.
(The easiest way to satisfy dependencies is to install Xcode command line tools,
the gcc compiler 4.7 or higher using MacPorts, and possibly GMP 6.0.0 if needed.
Note that the version of the gcc included with Xcode is NOT sufficient.)
Rename
libgtfold_osx.a -> libgtfold.a
and follow the rest of directions.

To compile on a Unix/Linux machine, make sure the following files are in the
same directory:
--main.c
--profile.h
--profile.c
--summaryGraph.c
--summaryGraph.h
--hashtbl.c
--hashtbl.h
--Makefile
--graph.c
--graph.h
--memoryDFS.c
--memoryDFS.h
--libgtfold.a
--include folder with header files

Open a terminal window, navigate to the directory that contains
the above files, and type 'make' to compile the program.

To run, you will need to input a sequence file, and optionally a
structure file either in sfold (using -sfold option) or in gtboltzmann 
(using -e option) format.

Usage (from within that same directory): 
./RNAprofile [options] [seq file] 

Common options:
-v = verbose output that gives all helix classes and profiles with frequencies
-h [percent] = filter out all helix classes that occur in less than [h] percent
 of the input sample structures
-p [percent] = filter out all profiles that occur less than [p] percent of the
 input sample structures
-g = disable graph making component of program (if only interested in helix and
 profile stats)
-o [file name] = produces the output graphviz dot file called [file name];
 'profile.dot' used by default
-e [file] gtboltzmann style structure file as input
-sfold [file] Sfold style structure file as input