silOperon modularity and phylogenetic analysis

This repository contains the reproducible files for the silOperon manuscript prepared for Network Modeling Analysis in Health Informatics and Bioinformatics.

Contents

• data/input/: HMM profiles, protein FASTA files, and alignment files used in the sil gene analyses.
• scripts/: reproducible scripts for MAFFT, trimAl, IQ-TREE2/IQ-TREE, and HMMER reruns.
• data/trees_iqtree2/: maximum-likelihood gene trees and IQ-TREE reports.
• data/itol_datasets/: iTOL-ready tree and annotation files for silA, silP, and silR.
• results/figures/: publication-ready Figure 3 files with white background.
• results/tables/: supplementary tables S1-S4.

Reproducing the phylogenetic analysis

conda env create -f environment.yml
conda activate siloperon_phylogeny
bash scripts/01_run_publication_phylogeny_iqtree2_FINAL.sh data/input SILOPERON_IQTREE2_PUBLICATION_OUTPUT

If your conda installation provides iqtree rather than iqtree2, either create a symbolic link or edit the script to call iqtree.

Citation and data availability

Please cite the final published manuscript when available. All scripts and processed files should be archived in a public repository and assigned a DOI through Zenodo before final journal submission, if possible.