neffy - v0.1.1

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).

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📖 Documentation & Examples

📂 Example scripts are available in the repository.
📖 Full documentation: NEFFy Documentation.

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🔗 Archival DOI

To ensure long-term accessibility and reproducibility, NEFFy has been archived with a DOI:
🔗 Zenodo DOI: 10.5281/zenodo.14908220

- C++
Published by Maryam-Haghani about 1 year ago