neffy 0.1.2

A Python interface of NEFFy C++ tool: NEFF Calculator and MSA File Converter

NEFFy: NEFF Calculator and MSA File Converter

NEFFy is a versatile and efficient tool for bioinformatics research, offering advanced features for calculating NEFF (Normalized Effective Number of Sequences) for Multiple Sequence Alignments (MSA)s of any biological sequences, including protein, RNA, and DNA across various MSA formats.
Additionally, NEFFy includes built-in support for format conversion, allowing users to seamlessly convert between different MSA formats.

Python Library

Neffy also provides a python library as an interface of the executable files.

Library Usage

An example of neff computation:

cd example
python compute_neff.py

You can find more examples of using the Python library's various methods for NEFF calculations in the examples directory. For method parameters and detailed explanations, please refer to the documentation usage guide.

An example of MSA conversion:

cd example
python convert_msa.py

Additional examples of using NEFFy for MSA conversion can be found in the example directory. For further detailed explanations, please refer to the documentation usage guide.

Supported File Formats

• A2M (aligned FASTA-like format)
• A3M (compressed aligned FASTA-like format with lowercase letters for insertions)
• FASTA, AFA, FAS, FST, FSA (FASTA format)
• STO (Stockholm format)
• CLUSTAL (CLUSTAL format)
• ALN (ALN format)
• PFAM (format mostly used for nucleotides)

In the documentation, you will find a brief explanation of each format, along with an illustrative alignment example for each one.

Error Handling

If any errors occur during the execution of the MSA Processor, an error message will be displayed, describing the issue encountered.
Please refer to the error message for troubleshooting or make necessary corrections to the input.

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.

Citation

If you use NEFFy in your research, please cite the following:

Maryam Haghani, Debswapna Bhattacharya, T M Murali, NEFFy: A Versatile Tool for Computing the Number of Effective Sequences, Bioinformatics, 2025; https://doi.org/10.1093/bioinformatics/btaf222

Archival DOI

For long-term accessibility and reproducibility, each release of NEFFy is archived with a DOI:

Version	DOI
Latest (v0.1.2)	🔗 Zenodo DOI: 10.5281/zenodo.14908220

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For further assistance, please see the documentation.