Results for “phylogenetic-tree”

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

绘制研究领域或技术主题的谱系脉络与历史演进图，可视化思想的演化路径，展示早期工作中的技术难题如何被后续研究逐步解决。当用户想了解某个主题的发展轨迹、某个模型或技术的"家族树"（family tree）、某条研究线索在多年间的演进路线、技术迭代脉络、论文/模型谱系，或询问"X 是如何一步步发展来的""X 解决了前人的什么问题""梳理 X 的发展历史"时触发。产出为嵌入 Mermaid 图表的 Markdown 文件（演进图 + 节点明细表 + 阶段叙事），可直接粘贴至 Mermaid 查看器或提交至代码仓库。

Systematic framework for resurrecting and modernizing legacy codebases through archaeology, resurrection, and rejuvenation phases. Activate on "legacy code", "inherited codebase", "no documentation", "technical debt", "resurrect", "modernize". NOT for greenfield projects or well-documented active codebases.

Generate knowledge schemas and ontologies from any input format. Extract semantic structures, relationships, and hierarchies. Output as Obsidian markdown with YAML frontmatter, wikilinks, tags, and mermaid diagrams, or export to semantic formats (JSON-LD, RDF, Neo4j Cypher, GraphQL). Supports fractal mode (strict hierarchical constraints) and free mode (flexible generation). Auto-activates for queries containing "schema", "ontology", "knowledge graph", "extract structure", or "generate outline".