http://xgenes.com/article/article-content/371/identify-all-occurrences-of-phage-hh1-mt880870-in-s-epidermidis-st2-genomes-from-public-and-clinical-isolates/

1. Downloads gff

    #for id in CP009257.1 CP000521.1 CP059040.1 CU459141.1 CU468230.2 CP141284.1 CP131470.1 CP002080.1 CP002177.1 CP041365.1; do
    #  efetch -db nuccore -id ${id} -format gff3 > ${id}.gff;
    #  efetch -db nuccore -id ${id} -format fasta > ${id}.fasta;
    #done
   
    echo -e "CP009257\nCP000521\nCP059040\nCU459141\nCU468230\nCP141284\nCP131470\nCP002080\nCP002177\nCP041365\nCP191205" > ids.txt
   
    cat ids.txt | while read id; do
        efetch -db nuccore -id $id -format gff3 > "${id}.gff"
        efetch -db nuccore -id $id -format fasta > "${id}.fasta"
        # Append the FASTA sequence to the GFF3 file with ##FASTA header
        echo "##FASTA" >> "${id}.gff"
        cat "${id}.fasta" >> "${id}.gff"
        rm "${id}.fasta"  # Optionally remove the separate FASTA file

2. Roary

    mv *.gff roary_input
    (bacto) roary -f roary_out -e --mafft -p 100 roary_input/*.gff

3. Generate phylogenetic tree using FastTree or raxml

    #iqtree -s core_gene_alignment.aln -m GTR+G -bb 1000 -nt AUTO
   
    (bacto) FastTree -nt roary_out/core_gene_alignment.aln > roary_out/core_gene_tree.nwk
   
    (bacto) raxml-ng --all \
      --msa roary_out/core_gene_alignment.aln \
      --model GTR+G \
      --bs-trees 1000 \
      --threads 40 \
      --prefix core_gene_tree_1000
   
      运行完后，你会得到：
   
      core_gene_tree_1000.raxml.bestTree : 最佳最大似然树。
      core_gene_tree_1000.raxml.bootstraps : 100 个 bootstrap 树。
      core_gene_tree_1000.raxml.support : 带有 bootstrap 支持值的树（就是你要的）。

4. Install ete3_env

    mamba create -n ete3_env python=3.10 ete3 -c etetoolkit -y
    mamba activate ete3_env
    mamba install -c etetoolkit ete3 pyqt

5. Phylogenetic Tree Visualization using ete3

    #(ete3_env) python3 ~/Scripts/label_tree.py roary_out/core_gene_tree.nwk
    (ete3_env) python3 ~/Scripts/label_tree.py core_gene_tree_1000.raxml.support
   
    #!/usr/bin/env python3
   
    from ete3 import Tree, TreeStyle, TextFace, NodeStyle, faces
    import sys
   
    #(ete3_env) jhuang@WS-2290C:~/DATA/Data_Tam_DNAseq_2025_AYE/REVIEW$ python3 ~/Scripts/label_tree.py core_gene_tree_1000.raxml.support
   
    # -------------------------
    group_colors = {
        "A. baumannii": "#1f77b4",
        "A. junii": "#ff7f0e",
        "A. pittii": "#2ca02c",
        "A. oleivorans": "#d62728",
        "A. tandoii": "#9467bd",
    }
   
    leaf_name_map = {
        "CP191205": "A. baumannii HKAB-1",
        "CP009257": "A. baumannii AB030",
        "CP000521": "A. baumannii ATCC 17978",
        "CP059040": "A. baumannii ATCC 19606",
        "CU459141": "A. baumannii AYE",
        "CU468230": "A. baumannii SDF",
        "CP141284": "A. junii H1",
        "CP131470": "A. junii SC22",
        "CP002080": "A. oleivorans DR1",
        "CP002177": "A. pittii PHEA-2",
        "CP041365": "A. tandoii SE63"
    }
   
    def get_group(label):
        for group in group_colors:
            if label.startswith(group):
                return group
        return "Other"
   
    def colorize_node(node):
        if node.is_leaf():
            label = leaf_name_map.get(node.name, node.name)
            node.name = label
            group = get_group(label)
            color = group_colors.get(group, "black")
            face = TextFace(label, fsize=8, fgcolor=color)
            face.margin_left = 5  # <-- add margin to move label right from the point
            faces.add_face_to_node(face, node, column=0)
   
            nstyle = NodeStyle()
            nstyle["fgcolor"] = color
            nstyle["shape"] = "circle"
            node.set_style(nstyle)
   
    def render_tree(tree, filename, title="", circular=False):
        ts = TreeStyle()
        ts.mode = "c" if circular else "r"
        ts.show_leaf_name = False
        ts.title.add_face(TextFace(title, fsize=12, bold=True), column=0)
        ts.layout_fn = colorize_node
        ts.show_scale = True
        ts.branch_vertical_margin = 0
   
        # Customize scale bar:
        #ts.scale_len = 0.05  # Scale bar length in tree units
        #ts.scale_format = "%.2f"  # Format scale label to 2 decimals
   
        # Add a TextFace to show the scale you want
        #scale_face = TextFace("Scale: 0.05 substitutions/site", fsize=8)
        #ts.title.add_face(scale_face, column=1)
   
        tree.render(filename, w=1200, h=1200 if circular else 800, tree_style=ts)
   
    def main():
        if len(sys.argv) != 2:
            print("Usage: python3 label_tree.py 

   “) sys.exit(1) newick_file = sys.argv[1] try: with open(newick_file, “r”) as f: nwk_str = f.read().strip() if not nwk_str.endswith(“;”): nwk_str += “;” t = Tree(nwk_str, format=1) except Exception as e: print(f”[ERROR] Failed to load tree: {e}”) sys.exit(1) # Attempt to reroot at outgroup try: outgroup = t&”CP041365″ if outgroup != t: t.set_outgroup(outgroup) else: print(“[!] Outgroup is root already; skipping reroot.”) except Exception as e: print(f”[!] Warning: Could not reroot tree at baumannii clade: {e}”) #render_tree(t, “tree_colored_bootstrap.png”, title=””, circular=False) render_tree(t, “tree_colored_bootstrap.svg”, title=””, circular=False) print(“✅ Saved: tree_colored_bootstrap.svg”) if __name__ == “__main__”: main()