RASCAL is a tool designed to realign multiple sequence alignments. It was originally developed with an older version of the C/C++ standard. With the recent transition to C++11, the software required certain adjustments to ensure compatibility.
The original source code was available through an FTP server, which is now inaccessible. However, we obtained version 1.34 of the code from here, and made the necessary updates to ensure compatibility with modern compilers and C++11 features.
Due to the upgrade of the C++11, certain functions in RASCAL required modification to align with the new standard. These adjustments were made to ensure seamless execution in the updated C++ environment.
- Clone the repository:
git https://github.com/smilida/rascal.git
cd rascal- Compile the software:
cd src
make
cd cluspack
make- In the file named 'rascal', change the RASCAL and CLUSPACK path to respectively point to the directory containing the rascal and cluspack executables.
./rascal input_file output_fileIf you encounter any issues with the software, please ensure:
- Your compiler supports the C++11 required.
- All dependencies are properly installed.
If you use this software, please cite:
Thompson JD, Thierry JC, Poch O. RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics. 2003 Jun 12;19(9):1155-61. doi: 10.1093/bioinformatics/btg133. PMID: 12801878.
If you would like to contribute to the development of RASCAL, feel free to fork the repository and submit a pull request. Please make sure to follow the code style guidelines and ensure that all tests pass before submitting your contributions.