ilund4u 0.1.4.2

description

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: 0.1.4.2 (Jan 2025)

Detailed documentation with user guide is available at iLund4u Homepage

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

Contact

Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
You can also use Discussions section for sharing your ideas or feature requests!

Authors

iLund4u is developed by Artyom Egorov at the Atkinson Lab, 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.