RNApbfold - RNA folding with soft constraints
=============================================

This repository contains the implementation of the algorithm described
in Washietl et al. "RNA Folding with Soft Constraints: Reconciliation
of Probing Data and Thermodynamic Secondary Structure Prediction"
(submitted). At the moment, it is a clone of the Vienna RNA package
with an additional executable RNApbfold.

To compile RNApbfold follow the instructions:

Download the tar.gz package from https://github.com/downloads/wash/probing/RNApbfold-0.1.tar.gz

tar xzf RNApbfold-0.1.tar.gz
cd RNApbfold-0.1
./configure
make

The executable can be found in Progs/RNApbfold. Run

RNApbfold --help

for instructions how to use the program.

IMPORTANT:

* RNApbfold requires the GNU scientific library (GSL). On Ubuntu Linux
  you can install them like that:

  sudo apt-get install libgsl0-dev

  Packages for all other major distributions are available. Make sure
  you install the 'development' version including the header files
  required to compile RNApbfold.

* Don't run "make install" because it would overwrite an existing
  installation of the Vienna RNA package or install a non official
  version along with RNApbfold.