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A self-evolution engine for AI agents. Analyzes runtime history to identify improvements and applies protocol-constrained evolution. Communicates with EvoMap Hub via local Proxy mailbox.
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Large-scale data migrations with validation, rollback, and zero-downtime strategies. Activate on: data migration, database migration, zero-downtime migration, dual-write, backfill, cutover, data validation, schema migration. NOT for: schema evolution in streams (use schema-evolution-manager), API versioning (use api-versioning-backward-compatibility).
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Great Expectations, dbt tests, anomaly detection, and data contracts for data quality. Activate on: data quality, data validation, Great Expectations, data contract, anomaly detection, SLA, freshness check, schema validation. NOT for: dbt model structure (use dbt-analytics-engineer), schema evolution (use schema-evolution-manager).
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API migration strategies, deprecation workflows, and header/URL/content versioning. Activate on: API versioning, backward compatibility, deprecation, breaking change, API migration, v1 v2, sunset header. NOT for: schema evolution in data (use schema-evolution-manager), gateway routing (use api-gateway-reverse-proxy-expert).
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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.
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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.
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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.
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AutoResearch-inspired self-evolution loop for ANY Claude Code skill. Finds flaws, fixes them, benchmarks against a diverse prompt pool (anti-overfitting), and uses blind A/B judging. Fully automated — no human input needed during the loop.
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Expert-level stellar physics covering stellar structure and evolution, nucleosynthesis, stellar atmospheres, variable stars, binary systems, and stellar populations.
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Solves complex, open-ended problems using a knockout tournament mechanism. Generates an initial population of diverse candidate answers, pairs them into head-to-head matches, produces a hybrid "child" solution from each pair, and advances the best of the three through a bracket until a winner emerges. Use this skill whenever the user wants to competitively select the best answer from a field of alternatives, asks for a "tournament" or "bracket" style search, wants a faster alternative to full evolutionary search, or uses phrases like: "run a tournament on this", "bracket-style search", "let solutions compete", "knockout search", "find the best answer by elimination", or "which solution wins?". Also trigger when the problem is open-ended and the user wants a clear winner quickly rather than a deep multi-generation refinement.
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Use for the self-evolving civilization - skills, memories, swarm agents, energy economy, grid duels, metacognition. Run `python scripts/autonomous_loop.py --loop` from the repo root (or `darwin_engine.py --full` for skill evolution only).
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Evolutionary file renaming with wrapper files. Enables renames without hard breaks — references are organically updated through usage.
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Evolutionary file renaming with wrapper files, plus the terse MOVED-stub standard for whole folder/file moves. Enables renames without hard breaks — references are organically updated through usage.
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Orchestrator for agent harness work — the setup that makes AI agents follow project rules and improve when they fail. FIRES PROACTIVELY when agents misbehave, repeat mistakes, ignore instructions, skip skills, or when AGENTS.md exists but docs/harness/manifest.json is missing. Also triggers on: harness engineering, agent scaffold, agent keeps failing, agent not following instructions, make agents reliable, agents going off rails, agent forgot context, improve agent setup, self-improving agents, agents keep making mistakes, why is my agent bad, agent quality, agent setup broken, agents ignore skills, same mistake again, fix agent behavior, tune agent instructions, set up agent infrastructure, after project setup agents still bad. Routes bootstrap vs evolution. Not multi-agent topology — agent-builder.
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Evolve prompts/regex/SQL/code with Imbue's evolution loop.
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根据评分标准反复改进提示词、正则表达式、SQL和短代码。由AI生成候选方案，利用失败示例继续修正，并通过日志和快照查看结果。
Set up, debug, and extend PicoClaw using its own commands and configuration structure. Get guidance on model authentication, external tool connections, scheduled tasks, and how conversations are routed and stored.
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Turn an OpenAPI specification into starter code for an MCP server, which connects AI agents to API tools. Support Python or TypeScript implementations, validate tool definitions, and plan changes that preserve compatibility.
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Helps founders and first-time CEOs review delegation, calendar use, energy, and leadership blind spots. Provides frameworks and reflection questions for adapting their role as the company grows, addressing burnout concerns, and preparing others to take over responsibilities.
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Extends the core PUA skill with local performance notes, recovery of task state after conversation compression, KPI report cards, and style switching. It tracks established working habits across sessions and keeps feedback in a local file.
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Save decisions, research findings, and work updates to Obsidian, then update related notes, daily entries, and task boards. Maintain existing pages, preserve changing facts with their history, and check for duplicates and broken links.
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Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
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Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.
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