RNAstructure

• available from the Mathews lab at https://rna.urmc.rochester.edu/RNAstructure.html
• fealden requires the "text" interface version, for your operating system
• has a python_interface available, but requires C++ compilation step
• RNAstructure version 6.4 needs corrections in rna_sources.h in the python_interface folder:
  • all references to TurboFold directory need to be replaced with src directory
  • can use command sed -i 's/TurboFold\/src\//g' rna_sources.h to correct
• requires installation of swig
  • such as pip install swig or conda install swig
• once swig installed and rna_sources.h corrected, enter the python_interface directory and run:
  • make swig
  • make interface-from-distutils
  • update .env file (see below) with path to RNAstructure

UNAfold and mfold

• version 3.8 of UNAfold is available from sourceforge: https://rnaspace.sourceforge.net/software/unafold-3.8.tar.gz
• once unzipped, enter the unafold-3.8 directory and run:
  • ./configure --prefix=/A/GOOD/PATH/FOR/USER (for instance, /home/user/unafold-final)
  • make
  • make install
  • update .env file (see below) with path to HYBRID_SS_MIN in Unafold
• You will also need the program sir_graph included in version 3.6 of mfold, available at http://www.unafold.org/download/mfold-3.6.tar.gz
• once unzipped, enter the mfold-3.6 directory and run:
  • ./configure --prefix=/A/GOOD/PATH/FOR/USER (for instance, /home/user/mfold-final)
  • make
  • make install
  • update .env file (see below) with path to SIR_GRAPH in Unafold

FEALDEN_BACKEND=mfold   # either 'mfold' or 'rnastructure'
HYBRID_SS_MIN=/home/username/unafold-new/bin/hybrid-ss-min
SIR_GRAPH=/home/username/mfold/bin/sir_graph
RNASTRUCTURE=/home/username/RNAstructure