Knotergy: Pseudoknotted RNA Secondary Structure Energy Evaluator

Compute Gibbs free energy for RNA secondary structures, including pseudoknots

Knotergy is a C++ bioinformatics tool for calculating the Gibbs free energy (ΔG) of RNA secondary structures, including pseudoknots.
It uses the ViennaRNA library for non-pseudoknotted calculations.

System Requirements

Supported Operating Systems

• Linux (64-bit)
• macOS (64-bit)

Software Requirements

• CMake ≥ 3.15
• ViennaRNA = 2.7.0

---

1. Install ViennaRNA

Knotergy requires ViennaRNA to compile and run.

1. Download ViennaRNA 2.7.0:

   curl -L -O https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.7.0/ViennaRNA-2.7.0.tar.gz

2. Install:

   tar -zxvf ViennaRNA-2.7.0.tar.gz
   cd ViennaRNA-2.7.0
   ./configure --without-perl
   sudo make -j$(nproc)              # Linux
   sudo make -j$(sysctl -n hw.ncpu)  # macOS
   sudo make install

Common Installation Issues

• No admin access:

  mkdir -p ~/local
  ./configure --without-perl --prefix=$HOME/local
  make -j$(nproc)              # Linux
  make -j$(sysctl -n hw.ncpu)  # macOS
  make install

• Template error on some compilers (dlib fix):

  sed -i.bak 's/::template go(/::template go<>(/' src/dlib-19.24/dlib/global_optimization/find_max_global.h

For full details, see the ViennaRNA GitHub repo.

---

2. Install CMake

Knotergy requires CMake ≥ 3.15.

Check your current version:

cmake --version

Linux:

sudo apt update
sudo apt install cmake

macOS:

Install Homebrew first, then:

brew install cmake

---

3. Install Knotergy

Clone the repository

git clone https://github.com/TheCOBRALab/Knotergy.git
cd Knotergy

Alternatively, download the zip:

curl -L -O https://github.com/TheCOBRALab/Knotergy/archive/refs/heads/main.zip
unzip main.zip
cd Knotergy-main

Build

cmake -S . -B build
cmake --build build --parallel

Debug build:

cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug
cmake --build build --parallel

---

4. Usage

./build/Knotergy [flags]

Run --help for available options:

./build/Knotergy --help