Data for: DNRA horizontal gene transfer (HGT) analysis of nrfA genes

This dataset supports the manuscript on DNRA (dissimilatory nitrate reduction to ammonium) and horizontal gene transfer (HGT) analysis of nrfA genes.## Dataset Summary- **Total files**: 90 files- **Last updated**: 2026-05-13## Folder Structure| Folder | Content | File Count ||--------|---------|------------|| `01_sequences/` | FASTA sequence files with subdirectories (raw/, processed/, aligned/) and combined dataset | 10 files || `03_tree/` | Phylogenetic tree files (IQ-TREE outputs: .nwk, .fasta alignment) | 3 files || `04_hgt/` | HGT analysis results (GC content, ENC, delta GC, candidate lists, IQ-TREE outputs, metadata) | 14 files || `05_script/` | Python/Shell scripts for data retrieval, analysis, and figure generation (includes sub-modules: easy_fig/, flanking_mobile_elements/, generax_scripts/, reconciliation/) | 51 files || `06_figures/` | Raw CSV data used to generate figures and tables | 15 files |### Detailed Directory Tree```文件关联数据/│├── Readme.md│├── 01_sequences/│  ├── all_sequences.fasta│  ├── aligned/│  │  ├── nrfA_alignment.fasta│  │  ├── nrfA_all_for_phylogeny.fasta│  │  └── nrfA_merged_alignment.fasta│  ├── processed/│  │  ├── mobile_element_proteins.fasta│  │  ├── nrfA_hgt.fasta│  │  ├── nrfA_reference.fasta│  │  └── nrfA_sequences.fasta│  └── raw/│    ├── nrfA_from_eutils.fasta│    └── PRJNA1204190_nrfA_candidates.fasta│├── 03_tree/│  ├── nrfA_alignment.fasta│  ├── nrfA_merged_tree.nwk│  └── nrfA_tree.nwk│├── 04_hgt/│  ├── delta_gc_analysis.json│  ├── enc_analysis_complete.json│  ├── gc_analysis_results_corrected.json│  ├── nrfA_hgt_candidates.csv│  ├── nrfA_hgt_meta.csv│  ├── nrfA_hgt_results.csv│  ├── nrfA_ML.contree│  ├── nrfA_ML.iqtree│  ├── nrfA_ML.treefile│  ├── Table2_HGT_candidates.csv│  ├── wwtp_nrfA_delta_gc.csv│  ├── wwtp_nrfA_enc_results.csv│  ├── wwtp_nrfA_gc_results.csv│  └── wwtp_nrfA_HGT_summary.csv│├── 05_script/│  ├── 05_script_README_scripts.txt│  ├── 05_script_requirements.txt│  ├── cross_phylum_clusters.json│  ├── [analysis scripts *.py × 28]│  ├── easy_fig/             ← EasyFig synteny visualization│  │  ├── download_genbank_files.py│  │  ├── run_easyfig_v2.py│  │  ├── search_geobacter.py│  │  ├── search_kuenenia.py│  │  └── synteny_final.py│  ├── flanking_mobile_elements/     ← Flanking region & mobile element analysis│  │  ├── step1_fetch_flanking.py│  │  ├── step1b_diagnose_accessions.py│  │  ├── step2_flanking_corrected.py│  │  ├── step3_deep_flanking.py│  │  ├── step4_blast_mobile_elements.py│  │  └── step5_visualization.py│  ├── generax_scripts/         ← GeneRax ML-DTL reconciliation│  │  ├── build_family_file.py│  │  ├── extract_plausible_trees.py│  │  ├── pargenes_to_family_file.py│  │  └── scalasca_build.sh│  └── reconciliation/          ← DTL reconciliation & bootstrap│    ├── inspect_json.py│    ├── step1_build_species_tree.py│    ├── step2_reconciliation_core.py│    ├── step3_bootstrap_reconciliation.py│    └── step4_visualization_v2.py│└── 06_figures/  ├── Figure7_metadata.csv  ├── nrfA_dist_matrix_new.csv  ├── nrfA_flanking_analysis.csv  ├── nrfA_gc_analysis.csv  ├── nrfA_gc_codon_results.csv  ├── nrfA_metadata.csv  ├── nrfA_reference_analysis.csv  ├── sequences_table.csv  ├── Table1_complete_metrics.csv  ├── TableS1_sequence_metadata.csv  ├── TableS2_lineage_summary.csv  ├── wwtp_nrfA_delta_gc.csv  ├── wwtp_nrfA_enc_results.csv  ├── wwtp_nrfA_gc_results.csv  └── wwtp_nrfA_HGT_summary.csv## Software Requirements- Python 3.9+ (see `05_script/05_script_requirements.txt`)- IQ-TREE v2.2.0- MAFFT v7.5- GeneRax (Linux/WSL; `conda install generax -c bioconda`)## ContactFor questions: 434934032@qq.com