etetoolkit
仓库创建 2025年10月20日最近提交 5 小时前SkillHot 收录 20 天前
▸ 精选理由
面向系统发育研究者，集成树操作与图形输出。
▸ 风险提示
可能需访问外部生物数据库（如NCBI）并安装本地生物信息学依赖。
这个 Skill 做什么
用于系统发育树的构建、操作、演化事件分析与可视化。
用 ETE 4 对系统发育树做读写、注释、拓扑编辑、比较和可视化，支持 Newick/Nexus 格式、Robinson‑Foulds 比较、TreePattern 模式匹配和基因树事件分析。适合已有树文件需要比对、标注、裁剪或做出版级图时用。注意它不是从原始序列推断树，序列比对和建树要先完成。
▸ 展开 SKILL.md 英文原文
Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.
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安装 / 使用
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帮我安装这个 skill：https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/main/skills/etetoolkit/SKILL.md或 curl 直取 SKILL.md
curl -fsSL "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/main/skills/etetoolkit/SKILL.md"SKILL.MD 节选查看完整文件 ↗
# ETE Toolkit 4 ## Scope Use ETE 4 to work with an existing tree: - Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write Newick trees - Compare topologies and calculate phylogenetic distances - Find repeated subtree topologies with `TreePattern` - Analyze gene trees with `PhyloTree` - Query local NCBI or GTDB taxonomy databases - Explore large trees interactively with SmartView - Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview ETE does not replace sequence alignment or phylogenetic inference software. For raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or another inference tool; then load the resulting tree into
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