Metadata-Version: 2.2
Name: neffy
Version: 0.1.1
Summary: A Python interface of NEFFy C++ tool: NEFF Calculator and MSA File Converter
Home-page: https://github.com/Maryam-Haghani/NEFFy
Author: Maryam Haghani
Author-email: haghani@vt.edu
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: summary

# 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. <br>
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:
```bash
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](https://maryam-haghani.github.io/NEFFy/usage_guide.html#python_neff_main).


### An example of MSA conversion:
```bash
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](https://maryam-haghani.github.io/NEFFy/usage_guide.html#python_converter).

<br>

# 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](https://maryam-haghani.github.io/NEFFy/msa_formats.html), you will find a brief explanation of each format, along with an illustrative alignment example for each one.

<br>

# Error Handling
If any errors occur during the execution of the MSA Processor, an error message will be displayed, describing the issue encountered. <br/>
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](LICENSE.txt) file for details.

# Citation

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

**NEFFy: A Versatile Tool for Computing the Number of Effective Sequences**. Haghani, M., Bhattacharya, D., Murali, T. M. (2024).
*bioRxiv*. [https://www.biorxiv.org/content/10.1101/2024.12.01.625733v1](https://www.biorxiv.org/content/10.1101/2024.12.01.625733v1)


----------------
For further assistance, please see the [documentation](https://maryam-haghani.github.io/NEFFy/).
