Mobility and sequence diversity of the Hok bacterial toxin family

This archive contains the bioinformatics analyses used in:Mobility and sequence diversity of the Hok bacterial toxin family Each subdirectory contains:1. Jupyter notebooks for specific analysis steps.2. README files describing the purpose and outputs of each analysis.3. Input and output files generated by the notebooks. ------------------------------------------------------------ DIRECTORY STRUCTURE Escalera-Maurer_2026||-- bac_classification_fig3| Bacterial classification and plasmid vs chromosome analyses (Fig. 3)| |-- bac_classification.ipynb| |-- bac_classification_plasmid_VS_chromosome.ipynb| |-- README_bac_classification.txt| |-- README_bac_classification_plasmid_VS_chromosome.txt| |-- Fig3A_raw_data.csv| |-- raw_data_fig3C.csv| |-- assembly_refseq_chromosomes_uniques.csv| |-- 240404_bac_refseq_Ass_reports.txt| |-- gtdbtk.bac120.decorated.tree-taxonomy| |-- f__Vibrionaceae_pept.fasta| |-- boxenplot_PvC_count_per_Genus.svg| |-- hits_per_enter_genus.svg| |-- percent_hits_per_fam_PvC.svg||-- bac_phylo_tree| Phylogenetic analysis and tree annotation| |-- tree_analysis.ipynb| |-- README_tree_analysis.txt| |-- Enterobacteriaceae.tree.itol| |-- bar_annot_hok_numbers_Chr.txt| |-- bar_annot_hok_numbers_Plasmid.txt||-- clean_clusters| Clustering, reclustering and sequence curation| |-- recluster.ipynb| |-- clean_reclustered_table.ipynb| |-- README_recluster| |-- README_clean_reclustered_table| |-- hok_reannotation_script_CDS_SD_annot.py| |-- representatives.csv| |-- selected_clans.fasta| |-- T1TAdb.csv| |-- missing_T1TAdb_to_add.csv| |-- trimal_removed.fasta| |-- multiple CSV and FASTA intermediate files| || |-- clus60| | |-- _all_seqs.fasta| | |-- _cluster.tsv| | |-- _rep_seq.fasta| || |-- clus80| | |-- _all_seqs.fasta| | |-- _cluster.tsv| | |-- _rep_seq.fasta| || |-- clus90| |-- _all_seqs.fasta| |-- _cluster.tsv| |-- _rep_seq.fasta||-- clus60_analysis_refseq_fig1C| Cluster 60 analysis on RefSeq (Fig. 1C)| |-- clus_analysis_refseq.ipynb| |-- README_clus_analysis_refseq.txt| |-- itol_annotation_location_60cluster.txt| |-- itol_annotation_methodology_clus60.txt| |-- itol_annotation_unique_log_count_per_60cluster.txt| |-- unique_log_counts.txt| |-- location_percent.txt| |-- methods_marks.txt| |-- mixed_clus100.svg| |-- 250326_fake_clus60_tree_for_plotting.txt||-- clus60_analysis_refseq_PR_VR_figS7A| PR vs VR RefSeq cluster analysis (Fig. S7A)| |-- clus_analysis_refseq_PR_VR.ipynb| |-- README_clus_analysis_refseq_VR_PR.txt| |-- itol_annotation_location_60cluster.txt| |-- itol_annotation_methodology_clus60.txt| |-- itol_annotation_unique_log_count_per_60cluster.txt| |-- unique_log_counts.txt| |-- location_percent.txt| |-- methods_marks.txt| |-- mixed_clus100.svg| |-- clus100_PvC.svg| |-- search_methods_counts_clean.svg| |-- 250707_fake_clus60_tree_refseq_VR_PR.txt||-- islets_fig1B| Hok genomic islets analysis (Fig. 1B)| |-- hoks_near_hoks.ipynb| |-- README_islets.txt| |-- Fig3B_raw_data.csv| |-- hok_islets.svg| |-- hok_islets_chr_pl_genus.svg||-- self_search_fig1B| All-vs-all self search analysis (Fig. 1B)| |-- self_search.ipynb| |-- README_self_search.txt| |-- IMG_VR_PR_refseq_pept.fasta| |-- all2all_pident_hist.svg| |-- hok_queries/| |-- results/||-- upset_logo_statistics_figs1ADE| Upset plots, sequence logos and statistics (Figs. 1A, 1D, 1E)| |-- upset.ipynb| |-- logos.ipynb| |-- stats.ipynb| |-- README_upset.txt| |-- README_logos| |-- README_stats| |-- upset.svg| |-- aa_logo_*.svg| |-- nt_aa_logo_*.svg| |-- clean_pept_for_logo.fasta| |-- clean_pept_for_logo_aln.fasta