Etetoolkit 工作流

# ETE Toolkit 常用工作流 本文档提供了使用 ETE Toolkit 执行常见任务的完整工作流。 ## 目录 1. [基础树操作](#basic-tree-operations) 2. [系统发育分析](#phylogenetic-analysis) 3. [树比较](#tree-comparison) 4. [分类学集成](#taxonomy-integration) 5. [聚类分析](#clustering-analysis) 6. [树可视化](#tree-visualization) --- ## 基础树操作 ### 加载与探索树 python from ete3 import Tree # 从文件加载树 tree = Tree("my_tree.nw", format=1) # 显示 ASCII 表示 print(tree.get_ascii(show_internal=True)) # 获取基础统计信息 print(f"叶子节点数: {len(tree)}") print(f"总节点数: {len(list(tree.traverse()))}") print(f"树深度: {tree.get_farthest_leaf()[1]}") # 列出所有叶子节点名称 for leaf in tree: print(leaf.name) ### 提取与保存子树 python from ete3 import Tree tree = Tree("full_tree.nw") # 获取特定节点为根的子树 node = tree.search_nodes(name="MyNode")[0] subtree = node.copy() # 保存子树到文件 subtree.write(outfile="subtree.nw", format=1) # 提取单系进化枝 species_of_interest = ["species1", "species2", "species3"] ancestor = tree.get_common_ancestor(species_of_interest) clade = ancestor.copy() clade.write(outfile="clade.nw") ### 剪枝至特定分类群 python from ete3 import Tree tree = Tree("large_tree.nw") # 仅保留感兴趣的分类群 taxa_to_keep = ["taxon1", "taxon2", "taxon3", "taxon4"] tree.prune(taxa_to_keep, preserve_branch_length=True) # 保存剪枝后的树 tree.write(outfile="pruned_tree.nw") ### 树重根 python from ete3 import Tree tree = Tree("unrooted_tree.nw") # 方法 1: 按外群重根 outgroup = tree & "Outgroup_species" tree.set_outgroup(outgroup) # 方法 2: 中点重根 midpoint = tree.get_midpoint_outgroup() tree.set_outgroup(midpoint) # 保存重根后的树 tree.write(outfile="rooted_tree.nw") ### 使用自定义数据标注节点 python from ete3 import Tree tree = Tree("tree.nw") # 基于元数据向节点添加特征 metadata = { "species1": {"habitat": "marine", "temperature": 20}, "species2": {"habitat": "freshwater", "temperature": 15}, } for leaf in tree: if leaf.name in metadata: leaf.add_features(**metadata[leaf.name]) # 查询标注特征 for leaf in tree: if hasattr(leaf, "habitat"): print(f"{leaf.name}: {leaf.habitat}, {l"