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Analyze existing evolutionary trees and other hierarchical trees with ETE 4. Edit branches, add annotations, compare branching structures, explore large trees interactively, and render figures for publication using the appropriate optional visualization components.
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ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.
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Exhaustive problem space exploration using the MIT Synthetic Neurobiology "tiling tree" method. Partitions a problem into MECE (Mutually Exclusive, Collectively Exhaustive) subsets recursively via parallel subagents, then evaluates leaf ideas against specified criteria. Use when users say "tiling tree", "tile the solution space", "exhaustively explore approaches to", "what are all the ways to", or request a MECE breakdown of a problem. Requires orchestrating-chat-agents skill.
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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.
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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.
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Execute tasks through systematic exploration, pruning, and expansion using Tree of Thoughts methodology with meta-judge evaluation specifications and multi-agent evaluation
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Guides parallel exploration of multiple implementation approaches using git worktrees. Use when facing decisions with multiple valid paths. Triggers on: explore options, compare approaches, parallel exploration.
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Explore a feature or CLI, repair verified defects, review adversarially, and leave one existing or new PR ready for its authorized reviewer. Use for "explore X", "test and ship X", "run the pipeline on X", "stress-test X", or "take X through the full pipeline" when exploration and integration matter. Supports lean autonomous, structured economy (default), and explicit hard-gated runs. Routine checkpoints do not require user approval; actual founder, L4, security, schema and merge gates always apply. Not for a one-file edit with no exploration need. Uses scripts/state.sh for resumable checkpoints.
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Analyze project code, configuration, and documentation to build a graph for interactive architecture exploration. It maps components and dependencies, supports Japanese descriptions, and can update the analysis based on changes since the previous analyzed commit.
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Document how a research or coding session evolved after the work is complete. The skill extracts decisions, experiments, failed approaches, and claims into ara/ files, distinguishing user statements from AI suggestions and actions.
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Applies the reasoning of David Silver, lead researcher on AlphaGo and AlphaZero at DeepMind, to problems of AI design, reinforcement learning, and open-ended discovery. Use this skill whenever you are designing AI systems, evaluating learning algorithms, balancing exploration vs. exploitation, choosing research problems, or discussing how to break past human performance ceilings. Reach for this whenever the user asks about self-play, Monte-Carlo Tree Search, tabula rasa learning, AGI, or moving from human-curated data to autonomous experience. It helps shift the focus from hardcoding human knowledge to building systems that learn for themselves.
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The craft of weaving story into interactive systems where the player is both audience and author. This skill covers the unique challenges of game narrative: branching structures that respect player agency, environmental storytelling that rewards exploration, dialogue systems that feel alive, and the delicate balance between authored experience and emergent narrative. Unlike linear media, games don't tell stories TO players - they create the conditions for stories to emerge WITH players. The narrative designer's job is to build the scaffolding that supports infinite player-authored moments while maintaining coherent themes and emotional arcs. This skill synthesizes lessons from Disco Elysium's internal monologue as gameplay, Hades' death-as-narrative-engine, interactive fiction's branching mastery (Inkle, Twine), and procedural narrative pioneers like Dwarf Fortress. It addresses ludonarrative harmony, bark systems, cinematics that respect agency, and the "and therefore" test that separates plot from story. Use when "narrative design, game story, game writing, dialogue system, branching narrative, player choice, environmental storytelling, bark system, quest design, lore delivery, ludonarrative, interactive fiction, inkle, twine, dialogue tree, player agency, cinematic design, voice direction, localization, procedural narrative, narrative, game-writing, dialogue, branching, player-agency, environmental-storytelling, quest-design, voice-acting, localization, interactive-fiction, procedural-narrative, ludonarrative" mentioned.
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Select the right Python charting library (seaborn, matplotlib, graphviz) and produce publication-quality static visualizations. Use when creating charts, plots, graphs, diagrams, heatmaps, visualizations from data, or when choosing between matplotlib/seaborn/graphviz. Also triggers for network diagrams, flowcharts, dependency trees, state machines, and entity-relationship diagrams. For interactive browser-rendered charts or uploaded data exploration, defer to charting-vega-lite instead.
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Applies the reasoning of David Silver, lead researcher on AlphaGo and AlphaZero at DeepMind, to problems of AI design, reinforcement learning, and open-ended discovery. Use this skill whenever you are designing AI systems, evaluating learning algorithms, balancing exploration vs. exploitation, choosing research problems, or discussing how to break past human performance ceilings. Reach for this whenever the user asks about self-play, Monte-Carlo Tree Search, tabula rasa learning, AGI, or moving from human-curated data to autonomous experience. It helps shift the focus from hardcoding human knowledge to building systems that learn for themselves.
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Explore a feature or CLI, reproduce defects and record bounded findings. Use for "explore X", "find issues with X", or the exploration stage of feature- pipeline; standalone runs return findings without automatically expanding scope.
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Multi-agent collaboration plugin that spawns N parallel subagents competing on the same task via git worktree isolation. Agents work independently, results are evaluated by metric or LLM judge, and the best branch is merged. Use when: user wants multiple approaches tried in parallel — code optimization, content variation, research exploration, or any task that benefits from parallel competition. Requires: a git repo.
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Abductive analysis for qualitative interview data following Timmermans & Tavory. Guides you through theory-first analysis that recognizes anomalies and generates novel theoretical insights through systematic puzzle exploration.
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