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phylogenetics
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phy…
tooluniverse-protein-design-campaign
Run and review iterative protein binder design campaigns with multiple model families, structural and glycan checks, conditional pH hypotheses, resource-aware computation, and competition submission preparation. Use for ongoing candidate optimization or interpreting conflicting design evidence; not for simple structure retrieval or measured assay analysis.
tooluniverse-protein-design-campaign
Run and review iterative protein binder design campaigns with multiple model families, structural and glycan checks, conditional pH hypotheses, resource-aware computation, and competition submission preparation. Use for ongoing candidate optimization or interpreting conflicting design evidence; not for simple structure retrieval or measured assay analysis.
tooluniverse-protein-design-campaign
Run and review iterative protein binder design campaigns with multiple model families, structural and glycan checks, conditional pH hypotheses, resource-aware computation, and competition submission preparation. Use for ongoing candidate optimization or interpreting conflicting design evidence; not for simple structure retrieval or measured assay analysis.
bio-comparative-genomics-ortholog-inference
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…
bio-rna-structure-ncrna-search
Searches for non-coding RNA homologs and classifies RNA families with Infernal covariance models against Rfam, scoring sequence AND secondary-structure conservation jointly. Use when deciding whether a covariance model is the right tool versus BLAST/nhmmer (structured ncRNA versus lncRNA or mature miRNA); choosing the Rfam gathering threshold over a flat E-…
bio-tcr-bcr-analysis-immcantation-analysis
Reconstructs B-cell clonal families, quantifies somatic hypermutation and selection, and builds antibody lineage trees with the Immcantation R suite (alakazam, shazam, scoper, dowser, tigger) on AIRR-format BCR data. Use when deriving the clonal-clustering threshold from the distToNearest bimodal valley (never a hardcoded 0.15); choosing hierarchicalClones …
legal-document-drafting-formatting-alessandro-dardano
Produces properly-formatted legal documents in Word (.docx). The user provides the substantive content (instructions, attached files, project knowledge); the skill handles document architecture and formatting. * No precedent or template required * Seven document families: agreements, corporate documents, litigation, memos, employment, policies, corresp…
nist-800-53
NIST SP 800-53 Rev 5 compliance advisor — all 20 control families (AC, AT, AU, CA, CM, CP, IA, IR, MA, MP, PE, PL, PM, PS, PT, RA, SA, SC, SI, SR), Low/Moderate/High baseline selection, FIPS 199/200 system categorization, control tailoring and overlays, privacy controls (PT family), supply chain risk management (SR family), assessment procedures (SP 800-53A…
reggio-documentation-protocol
Design a pedagogical documentation protocol for making children's learning processes visible and shareable. Use when documenting learning, communicating with families, or planning next steps.
venice-crypto-rpc
Use Venice as a pay-per-call JSON-RPC proxy to 27 EVM, Starknet, and Solana networks. Covers the public GET /crypto/rpc/networks, POST /crypto/rpc/{network}, chain families and their explicit per-family method allowlists, the 1×/2×/4× method-tier pricing model (~$7e-7 per credit), the per-minute rate limit and per-user request serialization, idempotency key…
numerical-integration
Select and configure time integration methods for ODE and PDE simulations — choose among explicit Runge-Kutta, BDF, Rosenbrock, and Adams families, set relative and absolute error tolerances, implement adaptive step-size control with P/PI step-size controllers, plan IMEX operator splitting for mixed stiff and non-stiff terms, and estimate splitting errors. …
threejs-node-tsl
three.js node-based shading: Nodes API surface, NodeMaterial and MeshStandardNodeMaterial-style families, TSL (Three.js Shading Language) entry at TSL.html, WebGPURenderer pairing, and core PostProcessing (class) versus addon EffectComposer at a high level. Use when authoring shaders as graphs, using TSL builtins, compute-oriented nodes, or modern WebGPU pi…
threejs-webxr
WebXR integration for three.js: WebXRManager and XRManager on the renderer, session initialization patterns, VRButton and ARButton helpers, XRControllerModelFactory and hand model families, XREstimatedLight, XRPlanes, and related addon Webxr utilities. Use for immersive sessions and controller/hand tracking—not for standard desktop camera projection (threej…
cjis-reviewer
Assess AWS environments against CJIS Security Policy v6.0 (NIST 800-53 control families), perform gap analyses, and generate assessment reports to guide compliance readiness. Use this skill whenever a user wants to check CJIS readiness, prepare for a triennial CJIS audit, assess an AWS environment handling Criminal Justice Information (CJI), review architec…
analyzing-malware-family-relationships-with-malpedia
Use the Malpedia platform and API to research malware family relationships, track variant evolution, link families to threat actors, and integrate YARA rules for detection across malware lineages.
analyzing-ransomware-encryption-mechanisms
Analyzes encryption algorithms, key management, and file encryption routines used by ransomware families to assess decryption feasibility, identify implementation weaknesses, and support recovery efforts. Covers AES, RSA, ChaCha20, and hybrid encryption schemes. Activates for requests involving ransomware cryptanalysis, encryption analysis, key recovery ass…
analyzing-threat-landscape-with-misp
Analyze the threat landscape using MISP (Malware Information Sharing Platform) by querying event statistics, attribute distributions, threat actor galaxy clusters, and tag trends over time. Uses PyMISP to pull event data, compute IOC type breakdowns, identify top threat actors and malware families, and generate threat landscape reports with temporal trends.
An independently imported catalog with original authors, licenses and source links. Classification is not a security audit.
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