Browse Skills — Page 70

common-feedback-reporter

HoangNguyen0403/agent-skills-standard

Pre-write skill violation audit. Checks planned code against loaded skill anti-patterns before any file write. Use when writing Flutter/Dart code, editing SKILL.md files, or generating any code where project skills are active. Load as composite alongside other skills. When a violation is detected and Auto-fixed: YES, also load +common/common-learning-log to record the mistake.

common-git-collaboration

HoangNguyen0403/agent-skills-standard

Enforce version control best practices for commits, branching, pull requests, and repository security. Use when writing commits, creating branches, merging, or opening pull requests.

common-law-begriffe-uebersetzung

Klotzkette/claude-fuer-deutsches-recht

Übersetzt deutsche Wirtschaftsrechtsbegriffe nicht wörtlich, sondern funktional nach Zielrechtsordnung, Klauselzweck und Risiko.

common-law-bilingual-contract-review

Klotzkette/claude-fuer-deutsches-recht

Vergleicht deutsche und englische Vertragsfassungen auf Bedeutungsdrift, Rangfolge, Definitionskonflikte und Haftungsrisiken.

common-law-client-explainer

Klotzkette/claude-fuer-deutsches-recht

Erklärt Common-Law-Risiken für deutsche Business-Teams kurz, freundlich und ohne dogmatische Nebelmaschine.

common-law-contract-formation-consideration

Klotzkette/claude-fuer-deutsches-recht

Erklärt offer, acceptance, consideration, deed, promissory estoppel und UCC-Varianten ohne deutsche Gegenleistungsfalle.

common-law-false-friends-scanner

Klotzkette/claude-fuer-deutsches-recht

Findet missverständliche deutsch-englische Rechtsbegriffe und schlägt sichere Formulierungen für Verträge und Memos vor.

common-law-governing-law-jurisdiction

Klotzkette/claude-fuer-deutsches-recht

Prüft Rechtswahl, Gerichtsstand, forum, venue, service, arbitration und Durchsetzbarkeit aus deutscher UK US Perspektive.

common-law-humor-coach

Klotzkette/claude-fuer-deutsches-recht

Macht trockene Common-Law-Erklärungen leicht lesbar, ohne rechtliche Präzision oder professionelle Distanz zu verlieren.

common-law-interpretation-precedent

Klotzkette/claude-fuer-deutsches-recht

Hilft deutschen Juristen, Präzedenzfalllogik, ratio, obiter, stare decisis und Vertragsauslegung in UK USA nicht falsch zu lesen.

common-law-kommandocenter

Klotzkette/claude-fuer-deutsches-recht

Startet Common-Law-, UK-, US- und bilingual-drafting-Mandate mit Jurisdiktionscheck, False-Friends-Scan und Arbeitsplan.

common-law-litigation-discovery

Klotzkette/claude-fuer-deutsches-recht

Erklärt pleadings, discovery, disclosure, depositions, privilege, evidence und settlement aus UK US Sicht.

common-law-ma-commercial-drafting

Klotzkette/claude-fuer-deutsches-recht

Unterstützt SPA APA NDA LOI Disclosure Schedules und Commercial Agreements mit Common-Law-Risikomatrix.

common-law-quality-gate

Klotzkette/claude-fuer-deutsches-recht

Prüft jedes Common-Law-Arbeitsprodukt auf Jurisdiktion, Quellenstand, False Friends, UK US Trennung und Review-Bedarf.

common-law-remedies-damages-equity

Klotzkette/claude-fuer-deutsches-recht

Erklärt damages, specific performance, injunction, rescission, restitution, equitable relief und punitive damages risikobewusst.

common-law-representations-warranties-covenants

Klotzkette/claude-fuer-deutsches-recht

Ordnet reps, warranties, covenants, conditions, undertakings und indemnities in Transaktionsverträgen präzise ein.

common-law-simulation-negotiation

Klotzkette/claude-fuer-deutsches-recht

Simuliert UK US Vertragsverhandlungen, Issue Lists und Mandantengespräche mit False-Friends-Lernkurve.

common-law-surety-guarantee-indemnity

Klotzkette/claude-fuer-deutsches-recht

Unterscheidet Bürgschaft, Garantie, suretyship, guarantee, indemnity, primary obligation und accessory liability sauber.

common-law-ucc-sales-goods

Klotzkette/claude-fuer-deutsches-recht

Prüft Warenkauf, UCC, Sale of Goods Act, title, risk, warranties, perfect tender und remedies für Commercial Deals.

common-law-us-vs-uk-drafting

Klotzkette/claude-fuer-deutsches-recht

Trennt British English, English Law, US contract style, Delaware/New York-Konventionen und generisches Business-English.

common-learning-log

HoangNguyen0403/agent-skills-standard

Append a structured learning entry to AGENTS_LEARNING.md whenever an AI agent makes a mistake. Auto-activates as a composite skill when: a pre-write skill violation is detected and auto-fixed, or when the session retrospective finds a correction loop. Also triggers directly when the user corrects the AI mid-session. Use when: mistake, wrong, redo, that's not right, correction, my bad, fix that error, I made a mistake, agent error, learning log, log mistake, AGENTS_LEARNING.md

common-llm-security

HoangNguyen0403/agent-skills-standard

OWASP LLM Top 10 (2025) audit checklist for AI applications, agent tools, RAG pipelines, and prompt construction. Use when performing any security review touching LLM client code, prompt templates, agent tools, or vector stores.

common-mobile-animation

HoangNguyen0403/agent-skills-standard

Apply motion design principles for mobile apps covering timing curves, transitions, gestures, and performance-conscious animations. Use when implementing screen transitions, gesture-driven interactions, shared-element animations, or optimizing animation frame rates on iOS, Android, or Flutter.

common-mobile-ux-core

HoangNguyen0403/agent-skills-standard

Enforce universal mobile UX principles for touch-first interfaces including touch targets, safe areas, and mobile-specific interaction patterns. Use when building mobile screens, handling touch interactions, or validating safe area compliance.

common-mobile-visual-testing

HoangNguyen0403/agent-skills-standard

Standardizes mobile UI audits, RTL verification, and state-specific testing on iOS/Android.

common-observability

HoangNguyen0403/agent-skills-standard

Enforce structured JSON logging, OpenTelemetry distributed tracing, and RED metrics across backend services. Use when adding request correlation, setting up tracing spans, defining SLO burn-rate alerts, or instrumenting middleware.

common-owasp

HoangNguyen0403/agent-skills-standard

OWASP Top 10 audit checklists for Web Applications (2021), APIs (2023), and Mobile (2024). Use when performing any security review, PR review, or codebase audit touching web, mobile, or API code.

common-pentest-methodology

HoangNguyen0403/agent-skills-standard

PTES-aligned penetration testing methodology for backend, frontend, and mobile. Provides attack taxonomy, exploit techniques per vulnerability class, and platform-specific test matrices. Use when executing pentest workflow, planning security assessments, mapping attack surfaces, or building threat models.

common-performance-engineering

HoangNguyen0403/agent-skills-standard

Enforce universal standards for high-performance development. Use when profiling bottlenecks, reducing latency, fixing memory leaks, improving throughput, or optimizing algorithm complexity in any language.

common-product-requirements

HoangNguyen0403/agent-skills-standard

Standardize PRD discovery and drafting for product scope, user outcomes, requirement IDs, and acceptance criteria. Use when creating PRD, product requirements, feature specification, or acceptance criteria plan.

common-protocol-enforcement

HoangNguyen0403/agent-skills-standard

Enforce Red-Team verification and adversarial protocol audit. Use when verifying tasks, performing self-scans, or checking for protocol violations. Load as composite for all sessions.

common-security-audit

HoangNguyen0403/agent-skills-standard

Probe for hardcoded secrets, injection surfaces, unguarded routes, business logic flaws, and platform-specific weaknesses across backend (Node, Go, Java, Python, Rust), frontend (React, Angular, Vue), and mobile (iOS, Android, Flutter) codebases. Use when performing security audits, vulnerability scans, secrets detection, or penetration testing.

common-security-standards

HoangNguyen0403/agent-skills-standard

Enforce universal security protocols for safe, resilient software. Use when implementing authentication, encryption, authorization, input validation, secret management, or any security-sensitive feature across any language or framework.

common-sense-index-investing-bogle

simbajigege/book2skills

Apply John Bogle index investing rules for low-cost funds, asset allocation,

common-session-retrospective

HoangNguyen0403/agent-skills-standard

Analyze conversation corrections to detect skill gaps and auto-improve the skills library. Use after any session with user corrections, rework, or retrospective requests. After finding correction loops, also load +common/common-learning-log to persist mistake entries to AGENTS_LEARNING.md.

common-skill-creator

HoangNguyen0403/agent-skills-standard

Standardizes the creation and evaluation of high-density Agent Skills (Claude, Cursor, Windsurf). Ensures skills achieve high Activation (specificity/completeness) and Implementation (conciseness/actionability) scores. Use when: writing or auditing SKILL.md, improving trigger accuracy, or refactoring skills to reduce redundancy and maximize token ROI.

common-software-requirements

HoangNguyen0403/agent-skills-standard

Standardize SRS and FRS specifications for technical behavior, interfaces, data contracts, quality constraints, and verification mapping. Use when writing SRS, functional specification, system behavior requirements, API/data contracts, or non-functional thresholds.

common-store-changelog

HoangNguyen0403/agent-skills-standard

Generate user-facing release notes for the Apple App Store and Google Play Store by collecting git history, triaging user-impacting changes, and drafting store-compliant changelogs. Enforces character limits (App Store ≤4000, Google Play ≤500), tone, and bullet format. Use when generating release notes, app store changelog, play store release, what's new, or version release notes for any mobile app.

common-system-design

HoangNguyen0403/agent-skills-standard

Enforce separation of concerns, dependency inversion, and resilience patterns across layered and distributed architectures. Use when designing new features, evaluating module boundaries, selecting architectural patterns, or resolving scalability bottlenecks.

common-tdd

HoangNguyen0403/agent-skills-standard

Implements a strict Red-Green-Refactor loop to ensure zero production code is written without a prior failing test. Use when: creating new features, fixing bugs, or expanding test coverage.

common-telemetry

HoangNguyen0403/agent-skills-standard

Enforce tracking of token usage, execution metadata, and cost at the end of agent workflows. Use when a workflow concludes, before generating the final handoff or task.md artifact.

common-ui-design

HoangNguyen0403/agent-skills-standard

Design distinctive, production-grade frontend UI with bold aesthetic choices. Use when building web components, pages, interfaces, dashboards, or applications in any framework (React, Next.js, Angular, Vue, HTML/CSS).

common-web-visual-testing

HoangNguyen0403/agent-skills-standard

Standardizes visual audits, responsive design, and behavioral testing for web apps.

common-workflow-writing

HoangNguyen0403/agent-skills-standard

Rules for writing concise, token-efficient workflow and skill files. Prevents over-building that requires costly optimization passes. Use when creating or editing workflow files, SKILL.md files, or new skill definitions.

communicating-concisely

GanyuanRan/Aegis

Use when the user asks for caveman mode, fewer tokens, brief responses, compressed communication, or otherwise explicitly requests a much shorter answer.

communication

EliasOulkadi/shokunin

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communication-storytelling

lyndonkl/claude

Transforms analysis, data, and complex information into clear, persuasive narratives tailored to specific audiences — executives, customers, investors, or non-technical stakeholders. Provides story structures (Hero's Journey, Problem-Solution-Benefit, Situation-Complication-Resolution) and audience adaptation techniques. Use when presenting findings, explaining technical concepts to non-technical audiences, writing announcements, or when user mentions "write this for", "explain to", "present findings", "make this compelling", or "audience is".

communication-style

tzachbon/smart-ralph

Output rules for all agents - concise, scannable, actionable. Based on Matt Pocock's planning principles.

communications-getting-started

Significant-Gravitas/skills-catalog

Set up communications work from facts, spokespeople, approved messages, approval owners, and off-limits topics.

community-building

manojbajaj95/claude-gtm-plugin

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community-discovery

mkurman/zorai

When the user wants to find Slack groups, Discord servers, Reddit communities, forums, or online communities where their target audience hangs out. Also use when the user mentions "where to promote", "find communities", "community marketing", or "distribution channels".

community-forum

kostja94/marketing-skills

When the user wants to promote via forums, communities, or invite users to join a community. Also use when the user mentions "forum promotion," "Indie Hacker," "Hacker News," "community growth," "Discord promotion," "vertical community," "brand encyclopedia," "Wikipedia," "Quora," "Reddit community," "community building," "forum marketing," or "community invite." For Reddit copy, use reddit-posts. For strategy, use integrated-marketing.

community-launch-runner

aaron-he-zhu/aaron-marketing-skills

Use when the user asks to "launch on Product Hunt / Hacker News", "prepare community or directory launch submissions", or "plan the launch submission waves"; produces per-platform submission packages — a Product Hunt tagline / gallery / first-comment skeleton, a factual Show HN title and text, per-subreddit posts with a self-promotion rules table, tiered directory waves, and a regional channel matrix including Chinese communities — plus a platform red-line check (never solicit votes or organize voting rings) and T-0 submission-status lines for the launch registry. Not for paid amplification — use content-amplifier; not for creator channels — use campaign-planner; not for launch telemetry readouts — use launch-monitor; not for ongoing community presence or pre-launch karma-building outside the launch window — use participation-warmup-planner. 社区发布/PH提交包/Show HN/目录波次/平台红线/中文渠道

community-management-playbook

mohitagw15856/pm-claude-skills

Build a community management playbook for a brand's social media channels. Use when asked to create guidelines for managing comments, DMs, and community interactions, define a moderation policy, or build response frameworks for social media community managers. Produces a complete playbook with response templates, escalation paths, moderation rules, and tone guidelines.

community-marketing

mkurman/zorai

Build and leverage online communities to drive product growth and brand loyalty. Use when the user wants to create a community strategy, grow a Discord or Slack community, manage a forum or subreddit, build brand advocates, increase word-of-mouth, drive community-led growth, engage users post-signup, or turn customers into evangelists. Trigger phrases: \"build a community,\" \"community strategy,\" \"Discord community,\" \"Slack community,\" \"community-led growth,\" \"brand advocates,\" \"user community,\" \"forum strategy,\" \"community engagement,\" \"grow our community,\" \"ambassador program,\" \"community flywheel.\"

community-marketing

coreyhaines31/marketingskills

Build and leverage online communities to drive product growth and brand loyalty. Use when the user wants to create a community strategy, grow a Discord or Slack community, manage a forum or subreddit, build brand advocates, increase word-of-mouth, drive community-led growth, engage users post-signup, or turn customers into evangelists. Trigger phrases: \"build a community,\" \"community strategy,\" \"Discord community,\" \"Slack community,\" \"community-led growth,\" \"brand advocates,\" \"user community,\" \"forum strategy,\" \"community engagement,\" \"grow our community,\" \"ambassador program,\" \"community flywheel.\"

community-signals

gooseworks-ai/goose-skills

Extract leads from developer forums (Hacker News, Reddit) by detecting intent signals — alternative seeking, competitor pain, scaling challenges, DIY solutions, and migration intent. Scores users by intent strength and cross-platform presence.

comorbidity-common-immune-biomarker

aipoch/medical-research-skills

Generates complete comorbidity-oriented shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Use when a study links two clinically related diseases through shared DEGs, enrichment, PPI hub genes, machine-learning feature selection, public diagnostic validation, gene-regulatory networks, immune infiltration, and optional downstream follow-up. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, machine-learning biomarker selection, immune/regulatory interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

comp-analysis

anthropics/knowledge-work-plugins

Analyze compensation — benchmarking, band placement, and equity modeling. Trigger with "what should we pay a [role]", "is this offer competitive", "model this equity grant", or when uploading comp data to find outliers and retention risks.

comp-simulation

t0ddc3by/claude-for-customer-success

Models comp plan payout scenarios before plan is finalized. Stress-tests OTE, accelerators, and threshold structures against attainment distributions (50/65/75/85/100%). Surfaces cost-to-company and unintended payout behaviors. G3 applies — all outputs require HR + Finance dual review before rep distribution. Triggers: 'comp simulation', 'model comp payouts', 'comp plan cost', 'stress test comp plan', 'what does the plan cost at 80/100/120%'.

compact

catlog22/Claude-Code-Workflow

Compact current session memory into structured text for session recovery. Supports custom descriptions and tagging.

compact-guard

rohitg00/pro-workflow

Smart context compaction with state preservation. Saves critical files, task progress, and working state before compaction, restores after. Use before manual compact or when auto-compact triggers.

compact-memory-implementation

simbajigege/book2skills

Developer implementation guide for adding compact memory to an Agent — covers fork agent pattern for compaction, trigger strategy, summary format design, and memory restoration in subsequent sessions. Use when a developer asks how to implement compact memory, context compression, or memory persistence in their agent built with Claude Agent SDK or Anthropic API.

company-activity-summary

ComposioHQ/composio-plugin-cc

Generates comprehensive company activity summary across connected apps — Slack, GitHub, Notion, Linear, Gmail, and more. Uses the composio CLI to fetch data. Use when user asks for company updates, daily summary, or what's happening across the org.

company-announcement-writer

OneWave-AI/claude-skills

Executive communication style for all-hands emails. Balances transparency with appropriate messaging.

company-brain

coreyhaines31/makerskills

Your team's shared, AI-ready knowledge base — people, companies, meetings, SOPs, and decisions structured so an agent can answer on your team's behalf. Team-scope sibling to second-brain. Modes — capture, compile (wiki pages + INDEX.md), query (trust-weighted, saved to outputs/), review (verify / deprecate / supersede stale captures), lint, connect, search. Structured raw dirs (people/, companies/, meetings/, sops/, decisions/, customer-language/, sales-objections/). Every capture stamps author, timestamp, and trust status. Optional sync from call transcripts, Slack/email exports, CRM. Vault at ${COMPANY_BRAIN_VAULT:-$HOME/Documents/CompanyBrain}/. Triggers on "/company-brain," "/cb," "capture this into the team brain," "log this meeting," "save this SOP," "compile the company wiki," "query the team brain," "what does the team know about X," "review the company brain," "lint the company brain," "who's the internal expert on X."

company-cfo

coreyhaines31/makerskills

Monthly CFO workflow for a company or agency — pull raw data from bank + payment processor + payroll + expense management, categorize and reconcile, compute end-of-month cash via transaction-sum method, update a scenario projector for forward forecasting, write the monthly snapshot report, surface decisions to leadership. Modes — monthly (default; the standing report), weekly (thin cash pulse), scenario (ad-hoc modeling in the projector), pickup (resume where the prior run left off). Anonymized team-scope sibling to personal-cfo (which handles personal household finances). Composes with company-brain (report gets stored + wiki-indexed there), toolify (wire company-specific data sources), loopify (schedule the monthly + weekly runs). Triggers on "/company-cfo," "/cfo," "monthly cash report," "do the CFO snapshot," "CFO monthly," "let's run CFO," "cash projection," "runway forecast," "monthly financials," "cash pulse."

company-contact-finder

gooseworks-ai/goose-skills

>

company-creator

paperclipai/paperclip

>

company-creator

microsoft/amplifier-app-paperclip

>

company-current-gtm-analysis

gooseworks-ai/goose-skills

>

company-os

alirezarezvani/claude-skills

The meta-framework for how a company runs — the connective tissue between all C-suite roles. Covers operating system selection (EOS, Scaling Up, OKR-native, hybrid), accountability charts, scorecards, meeting pulse, issue resolution, and 90-day rocks. Use when setting up company operations, selecting a management framework, designing meeting rhythms, building accountability systems, implementing OKRs, or when user mentions EOS, Scaling Up, operating system, L10 meetings, rocks, scorecard, accountability chart, or quarterly planning.

company-policy-lookup

Significant-Gravitas/skills-catalog

Find and explain company policies in plain language. Trigger with "what's our PTO policy", "can I work remotely from another country", "how do expenses work", or any plain-language question about benefits, travel, leave, or handbook rules.

company-radar

Varnan-Tech/opendirectory

Competitive intelligence orchestrator tracking companies across 8+ platforms (GitHub, Twitter, Reddit, HN, PH, YC Jobs) with heat scores and AI briefings.

company-recording-clip

zapier/gtm-cheat-codes

Turn a company meeting or event recording into a short, approved, postable clip.

company-research

deanpeters/Product-Manager-Skills

Create a company research brief with executive quotes, product strategy, and org context. Use when preparing for interviews, competitive analysis, partnerships, or market-entry work.

company-tearsheet

openai/plugins

Use when creating source-backed public issuer tearsheets. Do not use for private diligence, fund diligence, vendors, or market maps.

company-values

TerminalSkills/skills

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company-wiki

aAAaqwq/AGI-Super-Team

Company knowledge base — domains, services, infrastructure, accounts, credentials locations, architecture decisions

comparable-apps

EpicenterHQ/epicenter

List 3-5 comparable apps when planning a UX surface to find asymmetric wins. Use for "what do other apps do", identity, sync state, local-first design.

comparative_drug_analysis

InternScience/scp

Comparative Drug Analysis - Compare drugs: structure analysis, PubChem data, FDA safety, and ChEMBL bioactivity. Use this skill for comparative pharmacology tasks involving ChemicalStructureAnalyzer get compound by name get adverse reactions by drug name search activity. Combines 4 tools from 4 SCP server(s).

comparative-feasibility-ranking

yogsoth-ai/de-anthropocentric-research-engine

Compare feasibility across multiple candidates using multi-dimensional radar and weighted feasibility index.

comparative-formulation

yogsoth-ai/de-anthropocentric-research-engine

Strategy: 构建对比性研究问题 — A vs B 的系统化比较

comparative-genomics-ancestral-reconstruction

swaruplab/operon

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.

comparative-genomics-comparative-annotation-projection

swaruplab/operon

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

comparative-genomics-gene-family-evolution

swaruplab/operon

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.

comparative-genomics-gene-tree-species-tree-reconciliation

swaruplab/operon

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

comparative-genomics-genome-distance-and-species-delineation

swaruplab/operon

Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

comparative-genomics-hgt-detection

swaruplab/operon

Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

comparative-genomics-introgression-detection

swaruplab/operon

Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

comparative-genomics-ortholog-inference

swaruplab/operon

Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

comparative-genomics-pangenome-analysis

swaruplab/operon

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

comparative-genomics-positive-selection

swaruplab/operon

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.

comparative-genomics-synteny-analysis

swaruplab/operon

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

comparative-genomics-whole-genome-alignment

swaruplab/operon

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.

comparative-genomics-whole-genome-duplication

swaruplab/operon

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DTL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

comparative-network-toxicology-shared-mechanism-reference-grounded

aipoch/medical-research-skills

Generates complete comparative network-toxicology research designs from a user-provided exposure pair, shared toxic phenotype, and validation direction. Use when a study centers on two related exposures under one outcome and needs target collection, shared-vs-specific target decomposition, enrichment, PPI hub prioritization, docking, optional transcriptomic cross-checks, and conservative mechanistic synthesis. Covers five study patterns and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

comparative-religion

Tibsfox/gsd-skill-creator

Comparative religion as a scholarly discipline — cross-tradition analysis of doctrines, practices, and experiences without collapsing traditions into each other or ranking them against a normative standard. Covers the history of the discipline (from Max Muller through Eliade, Smart, Smith, and the contemporary critique), typologies (theism, monism, polytheism, non-theism), the dimensions framework (doctrinal, ritual, ethical, experiential, mythic, institutional, material), and the ethics of comparison. Use when a query asks how a concept, practice, or text functions across multiple traditions.

comparison-design

yogsoth-ai/de-anthropocentric-research-engine

Design fair comparison experiments against baselines and competing methods

comparison-executor

yogsoth-ai/de-anthropocentric-research-engine

Execute a pairwise comparison between two candidates, producing a judgment with winner, confidence, and reasoning.