Metadata-Version: 2.4
Name: ilund4u
Version: 0.1.4
Summary: description
Home-page: https://art-egorov.github.io/ilund4u/
Author: Artyom Egorov
Author-email: artem.egorov@med.lu.se
License: WTFPL
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: LICENSE_dependencies
Requires-Dist: biopython
Requires-Dist: requests
Requires-Dist: configs
Requires-Dist: pandas
Requires-Dist: bcbio-gff
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: scipy
Requires-Dist: msa4u
Requires-Dist: lovis4u
Requires-Dist: progress
Requires-Dist: leidenalg
Requires-Dist: igraph
Requires-Dist: pyhmmer
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<img  src="https://raw.githubusercontent.com/art-egorov/iLund4u/main/docs/img/ilund4u_logo.png?token=GHSAT0AAAAAACNA6ZUMHKXAJEHFEYINLXQ2ZTK4Y3Q" width="310"/>

## Description

**iLund4u** is a bioinformatics tool for search and annotation of accessory genes and hotspots in a large set of proteomes. 

**Supported input**: gff3 for annotation files (prokka/pharokka generated); fasta for protein sequences        
**Programming language:** Python3   
**OS:** MacOS, Linux  
**Python dependencies:** biopython, bcbio-gff, scipy, configs, pandas, matplotlib, seaborn, progess, leidanalg, igraph. pyhmmer, msa4u, lovis4u    
**Python version:** >= 3.8  
**OS-level dependencies:** MMseqs2 (included in the package)  
**License:** WTFPL  
**Version:** 0.1.4 (October 2025)


**Detailed documentation with user guide is available at [iLund4u Homepage](https://art-egorov.github.io/ilund4u/)**


## Reference 

If you find iLund4u useful, please cite:  
Artyom. A. Egorov, Vasili Hauryliuk, Gemma C. Atkinson, **Systematic annotation of hyper-variability hotspots in phage genomes and plasmids**, *bioRxiv 22024.10.15.618418; doi: [10.1101/2024.10.15.618418](https://doi.org/10.1101/2024.10.15.618418)*

## Contact

Please contact us by e-mail _artem**dot**egorov**AT**med**dot**lu**dot**se_ or use [Issues](https://github.com/art-egorov/ilund4u/issues?q=) to report any technical problems.  
You can also use [Discussions section](https://github.com/art-egorov/ilund4u/discussions) for sharing your ideas or feature requests! 

## Authors

iLund4u is developed by Artyom Egorov at [the Atkinson Lab](https://atkinson-lab.com), Department of Experimental Medical Science, Lund University, Sweden. We are open for suggestions to extend and improve iLund4u functionality. Please don't hesitate to share your ideas or feature requests.
