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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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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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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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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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Use this skill for transporting heavy machinery (construction, agricultural, industrial). Covers § 393.130 rules, lashing requirements, and platform compliance.

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Expert landscape designer transforming yards through photo mapping, 3D visualization, seasonal planning, and deep plant knowledge. Specializes in fast-growing privacy screens (knows arborvitae pitfalls), architecture-appropriate design, outdoor living spaces, and realistic maintenance expectations. Activate on "landscape design", "yard design", "garden planning", "plant selection", "privacy screen", "outdoor living", "backyard makeover", "arborvitae", "hedge", "fast growing tree", "landscaping ideas". NOT for interior design (use interior-design-expert), hardscape construction (consult contractors), or lawn care chemicals (consult local experts).

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Advanced CV for infrastructure inspection including forest fire detection, wildfire precondition assessment, roof inspection, hail damage analysis, thermal imaging, and 3D Gaussian Splatting reconstruction. Expert in multi-modal detection, insurance risk modeling, and reinsurance data pipelines. Activate on "fire detection", "wildfire risk", "roof inspection", "hail damage", "thermal analysis", "Gaussian Splatting", "3DGS", "insurance inspection", "defensible space", "property assessment", "catastrophe modeling", "NDVI", "fuel load". NOT for general drone flight control, SLAM, path planning, or sensor fusion (use drone-cv-expert), GPU shader development (use metal-shader-expert), or generic object detection without inspection context (use clip-aware-embeddings).

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Design and implement systematic checklists that reduce errors by 30-50% in complex, high-stakes domains (medicine, aviation, construction, finance). NOT for simple tasks or when comprehensive instruction is needed.

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Conduct Critical Decision Method (CDM) interviews to elicit expert reasoning strategies (L3 knowledge) from practitioners about specific challenging past incidents. Use when capturing expertise for skill development, preserving knowledge before practitioner departure, building post-incident learning artifacts, or investigating decisions in complex sociotechnical systems. Outputs structured incident reconstructions with cues, decisions, alternatives considered, and counterfactual analysis suitable for distillation into skills or training material.

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Expert causal reasoning and mental model construction for diagnosis and prediction in complex domains

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AIエージェントのアクションスペース、ツール定義、オブザベーションフォーマットを設計・最適化し、タスク完了率を向上させる

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Generates Builder pattern for PHP 8.5. Creates step-by-step object construction with fluent interface and validation. Includes unit tests.

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Comprehensive toolkit for writing high-quality computer science research papers (conference, journal, thesis). Provides narrative construction guidance, sentence-level clarity principles (Gopen & Swan), academic phrasebank, CS-specific conventions, and section-by-section quality checklists. Use when assisting with academic paper writing, revision, or structure planning across all stages from drafting to submission.

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Complete Three.js building system with spatial indexing, structural physics, and multiplayer networking. Use for survival/crafting games, sandbox games, multiplayer construction, or any 3D building mechanics.

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[00] TnR ABSOLUTE RIGOR — Systemic Verification Doctrine. Forced cognitive exertion for high-stakes investigations. Mandates absolute deconstruction, mathematical proof chains, and ≥95% derived certainty. Zero-tolerance for heuristics or sentiment-based reasoning. Shortcuts are defined as intentional hallucinations.

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Turn a one-line objective into a step-by-step construction plan for multi-session, multi-agent engineering projects. Each step has a self-contained context brief so a fresh agent can execute it cold. Includes adversarial review gate, dependency graph, parallel step detection, anti-pattern catalog, and plan mutation protocol. TRIGGER when: user requests a plan, blueprint, or roadmap for a complex multi-PR task, or describes work that needs multiple sessions. DO NOT TRIGGER when: task is completable in a single PR or fewer than 3 tool calls, or user says "just do it".

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Design and optimize AI agent action spaces, tool definitions, and observation formatting for higher completion rates.

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Turn a one-line objective into a step-by-step construction plan any coding agent can execute cold. Each step has a self-contained context brief — a fresh agent in a new session can pick up any step without reading prior steps.

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Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.

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Complete guide for ASP.NET Core Web API integration testing. Use when performing integration testing on Web API endpoints or validating ProblemDetails error format. Covers WebApplicationFactory, IExceptionHandler, Testcontainers multi-container orchestration, Flurl URL construction, and AwesomeAssertions HTTP validation. Keywords: webapi integration testing, WebApplicationFactory, asp.net core integration test, webapi integration test, IExceptionHandler, ProblemDetails, ValidationProblemDetails, AwesomeAssertions, Flurl, Respawn, Be201Created, Be400BadRequest, multi-container testing, Collection Fixture, global exception handling

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AutoFixture and NSubstitute Integration Guide - Implementing Auto-Mocking. Use when you need to automatically create mock objects and simplify testing of complex dependency injection. Covers AutoNSubstituteDataAttribute, Frozen mechanism, Greedy construction strategy. Includes customized handling for special dependencies like IMapper (AutoMapper/Mapster). Keywords: autofixture nsubstitute, auto mocking, AutoNSubstituteDataAttribute, auto-mocking, Frozen, AutoNSubstituteCustomization, AutoFixture.AutoNSubstitute, Greedy, fixture.Freeze, Received(), Returns(), IMapper, AutoMapper, Mapster, mapper testing

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Build collaborative forensic incident timelines using Timesketch to ingest, normalize, and analyze multi-source event data for attack chain reconstruction and investigation documentation.

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Parses and analyzes the Windows Amcache.hve registry hive to extract evidence of program execution, application installation, and driver loading for digital forensics investigations. Uses Eric Zimmerman's AmcacheParser and Timeline Explorer for artifact extraction, SHA-1 hash correlation with threat intel, and timeline reconstruction. Activates for requests involving Amcache forensics, program execution evidence, Windows artifact analysis, or application compatibility cache investigation.

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Leverages Splunk Enterprise Security and SPL (Search Processing Language) to investigate security incidents through log correlation, timeline reconstruction, and anomaly detection. Covers Windows event logs, firewall logs, proxy logs, and authentication data analysis. Activates for requests involving Splunk investigation, SPL queries, SIEM log analysis, security event correlation, or log-based incident investigation.

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