「evolutionary」の検索結果

Think and work like an expert Evolutionary Biologist. Use when a task calls for Evolutionary Biologist judgment. Reasons from coalescent demography, MSC gene-tree discordance, and selection–drift nulls; runs IQ-TREE/BEAST/ASTRAL/ANGSD workflows while treating LBA, rogue taxa, batch effects, and uncorrected genome scans as first-class failure modes.

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Specialist in designing and implementing scalable modular monolith architectures using NestJS with DDD, Clean Architecture, and CQRS patterns. Use when building modular monolith backends, designing bounded contexts, creating domain modules, implementing event-driven module communication, or when user mentions "modular monolith", "bounded contexts", "module boundaries", "DDD", "CQRS", "clean architecture NestJS", or "monolith to microservices". Do NOT use for simple CRUD APIs, frontend work, general NestJS questions without architectural context, or stack-agnostic evolutionary modular monolith design (use evolutionary-modular-architecture).

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Guides design and implementation of evolutionary modular-monolith platforms with DDD (strategic + tactical), flat-by-aggregate organization, an Anti-Corruption Layer for vendor independence, a transactional outbox for events, smart resilience (backoff with jitter, circuit breakers, idempotency), and a polished architecture HTML document with elegant SVG diagrams. Use when designing a platform or backend, defining bounded contexts, organizing modules and folders, choosing monolith vs microservices, decoupling from an external service (ERP, storage, AI), making calls resilient, adding real-time push, picking a 2026 TypeScript stack (Nx, NestJS, React), or producing an architecture document or diagram. Also triggers on 'modular monolith', 'bounded contexts', 'flat-by-aggregate', 'ports and adapters', 'architecture diagram'. Do NOT use for simple CRUD, NestJS-only deep implementation (use nestjs-modular-monolith), or pure domain-model review (use tactical-ddd).

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Use when refactoring code with poor names, when asked to improve naming, or when a user struggles to name a class/method/variable. Symptoms include -Manager/-Util suffixes, single-letter variables, process/handle/do verbs, primitive obsession, god methods with multiple responsibilities. Two modes — audit (broad scan, list opportunities) and improve (walk one specific identifier through the process).

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Protein language models through the EvolutionaryScale `esm` Python SDK. Generate and embed sequences with ESM3 (multimodal sequence, structure and function prompting), extract per-residue and mean-pooled embeddings with ESM C, fold sequences with ESMFold2, and run inference locally or against the Forge and Biohub hosted clients. Use this skill for protein representation learning, variant effect and mutational scanning from likelihoods, sequence generation and inpainting, structure prediction from sequence alone, and embedding features for downstream models. Also trigger on esm, ESM3, ESMC, ESM Cambrian, ESMFold2, `from esm.models`, ESMProtein, GenerationConfig, forge.evolutionaryscale.ai, biohub.ai, or ESM_API_KEY.

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Expert-level evolutionary biology covering natural selection, genetic drift, molecular evolution, phylogenetics, speciation, macroevolution, and the modern synthesis.

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Establish or audit a structural quality contract for any agent-operated engineering repository: app, library, CLI/tool, plugin, harness, or meta repo. Use when a repo needs charter clarity, docs/decision ownership, type-native validation gates, evidence paths, safe action policy, cold-start legibility, maturity proof, repair-loop routing, consumer/producer owner-boundary routing, command surface evolution, evolutionary simplicity (see references/evolutionary-simplicity.md), or a repo ecology pass to decide what should be compressed, merged, removed, updated, created, retired, or moved to checks.

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Solves complex, open-ended problems using an evolutionary search mechanism inspired by genetic algorithms. Generates a diverse population of candidate answers, scores them against a rubric, then iteratively applies selection, crossover, and mutation to breed progressively better solutions. Use this skill whenever the user wants to explore a solution space deeply, asks for the "best" answer to a subjective or multi-dimensional problem, wants to evaluate competing approaches and distill the strongest, or uses any of these triggers: "evolutionary search", "genetic algorithm", "evolve an answer", "breed solutions", "population-based search", or phrases like "give me multiple approaches and refine the best one". Also trigger when the problem is complex, open-ended, or has no obvious single correct answer and the user wants a high-quality, well-explored result, not just a quick response.

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METAINFORMANT rules for directory src/metainformant/math/evolutionary_dynamics. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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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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Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports 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. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.

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Autonomous evolutionary code improvement engine with tournament selection

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Evolutionary ideation engine — loop-controlled multi-cycle idea generation through phases of dreaming, cross-domain stealing, recombination, fitness testing, selection, and Lamarckian meta-learning, producing ranked novel solution candidates with provenance. USE WHEN ideate, id8, novel ideas, evolve ideas, dream up solutions, innovate, breakthrough ideas, idea evolution, multi-cycle creativity, need genuinely new approaches. NOT FOR quick single-pass brainstorming (use BeCreative).

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Evolutionary explanation-discovery engine for hard-to-vary causal theories of unknown phenomena. USE WHEN develop a new theory, explain a mystery, solve an explanatory gap, discover a mechanism, consciousness, origin, or scientific breakthrough. Also use for multi-cycle creative exploration. NOT FOR a single-pass divergent brainstorm (use BeCreative) or delivery validation alone (use Evals).

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Divergent ideation and corpus expansion via Verbalized Sampling plus extended thinking — single-shot generates several internally diverse candidates and surfaces the strongest, or expands a seed corpus into a diverse dataset for evals and test sets. USE WHEN be creative, brainstorm, divergent ideas, creative solutions, maximum creativity, tree of thoughts, radically different, name this, creative angle, expand this corpus, synthetic data, generate diverse examples, create test set. NOT FOR multi-cycle evolutionary ideation with Lamarckian meta-learning (use Ideate).

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This skill should be used when the harness, scaffold, workflow, or optimizer itself is the optimization target: recursive self-improvement (RSI) loops, meta-harnesses, self-improving harnesses that mine their own failures and propose bounded edits, evolutionary or population-based search over agent scaffolds, acceptance gates for self-modifying systems, and agentic context evolution where the mechanism that produces context is versioned and evolved. Route governance of a single autonomous loop (locked surfaces, durable logs, rollback, novelty gates, approval boundaries) to harness-engineering, measurement and quality-gate design to evaluation, judge design to advanced-evaluation, and remote sandbox infrastructure to hosted-agents.

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Start or monitor an evolutionary development loop

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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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NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs (health.api.nvidia.com) on every call. Use local NIM containers for confidential or proprietary sequences. Run a complete protein structure prediction pipeline using NVIDIA BioNeMo NIMs: search for MSA alignments with MSA-Search (ColabFold), then predict the structure with OpenFold3 using the retrieved alignments. Use this skill whenever the user wants to predict a protein structure with maximum accuracy using MSA context, run the full AlphaFold3-style pipeline, generate MSA-informed structure predictions, or improve structure prediction accuracy by providing evolutionary information. Triggers on: MSA structure prediction pipeline, structure prediction pipeline, MSA-informed prediction, OpenFold3, ColabFold MSA, AlphaFold3 pipeline, protein structure, homology search, a3m alignment, UniRef30, NIM microservice. This pipeline chains MSA-Search and OpenFold3.

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Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolutionarily conserved, functionally important, or bounded by TF regulators across major projects (ENCODE, JASPAR, ReMap).

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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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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

日本語の概要は準備中です。原文の説明を表示しています。