NEFFy v0.1.1 - First Public Release 🎉
This is the first official release of NEFFy, a powerful and efficient bioinformatics tool for NEFF (Normalized Effective Number of Sequences) computation and MSA file format conversion.
🌟 Key Features
✅ NEFF Computation
- Computes the effective number of sequences (NEFF) in a Multiple Sequence Alignment (MSA).
- Supports protein, RNA, and DNA sequences.
- Offers multiple normalization options
- Provides per-residue NEFF computation.
- Supports multimer MSA calculations for complex structures.
✅ MSA File Format Conversion
- Converts MSA files between multiple formats, including:
- FASTA, A2M, A3M, STO, ALN, Clustal, PFAM.
- Built-in validation checks for input MSA files.
- Handles non-standard residues, and customizable similarity thresholds.
✅ Cross-Platform C++ Executable
- High-performance command-line tool.
- Supports Linux, Windows, and macOS.
✅ Python Library Integration
- Provides an easy-to-use Python API for NEFF computation and format conversion.
- Available on PyPI (
pip install neffy). - Installable via BioConda (
conda install -c bioconda neffy).
📖 Documentation & Examples
📂 Example scripts are available in the repository.
📖 Full documentation: NEFFy Documentation.
🔗 Archival DOI
To ensure long-term accessibility and reproducibility, NEFFy has been archived with a DOI:
🔗 Zenodo DOI: 10.5281/zenodo.14908220