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概要と使いどころ
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 phylogenies.
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Internal downstream skill for ctf-sandbox-orchestrator. CTF-sandbox workflow for custom binary or text protocol recovery, handshake reconstruction, framing, sequence control, checksums, stateful replay, and accepted-session reproduction. Use when the user asks to decode an unknown protocol, recover custom framing, build a replay harness, satisfy sequence or checksum rules, replay a captured session, or prove the smallest message order that reaches an accepted branch. Use only after `$ctf-sandbox-orchestrator` has already established sandbox assumptions and routed here.
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Build accretion/dilution analysis for M&A transactions. Models pro forma EPS impact, synergy sensitivities, and purchase price allocation. Use when evaluating a potential acquisition, preparing merger consequences analysis for a pitch, or advising on deal terms. Triggers on "merger model", "accretion dilution", "M&A model", "pro forma EPS", "merger consequences", or "deal impact analysis".
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When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value. Also use when the user mentions "onboarding flow," "activation rate," "user activation," "first-run experience," "empty states," "onboarding checklist," "aha moment," or "new user experience." For signup/registration optimization, see signup-flow-cro. For ongoing email sequences, see email-sequence.
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Ingest meeting transcripts from ANY meeting recorder into brain pages with attendee enrichment, entity propagation, and timeline merge. One unified pipeline: normalize the source into a standard transcript record, split multi-meeting recordings, resolve speakers by evidence, create the page, pass every surprising claim through the consistency check (transcript + brain + plausibility), enrich every entity, then run the verification checklist — substance AND sequence. A meeting is NOT fully ingested until the enrich skill has processed every entity AND the verification checklist passes, including the sequence verify (PASS or explicit user waive).
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Find leads matching criteria and bulk-add them to an Apollo outreach sequence. Handles enrichment, contact creation, deduplication, and enrollment in one flow.
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When the user wants to plan, promote, run, or improve a webinar or virtual event to generate and convert demand. Use when the user mentions 'webinar,' 'virtual event,' 'online event,' 'live demo,' 'virtual summit,' 'workshop,' 'masterclass,' 'fireside chat,' 'roundtable,' 'registration funnel,' 'show-up rate,' 'attendance rate,' 'webinar promotion,' 'webinar follow-up,' or 'on-demand webinar.' Also use when they have a webinar that isn't converting — low registrations, low show-up, or attendees who don't buy — and want to diagnose and fix it. Covers the full funnel: registration, promotion, show-up, live engagement, live-to-close, and post-event nurture. Distinct from launch-strategy (full product launches) and email-sequence (lifecycle nurture) — this is the end-to-end webinar/event motion. NOT for in-person field events logistics, and NOT for generic lifecycle email (use email-sequence).
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When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value. Also use when the user mentions "onboarding flow," "activation rate," "user activation," "first-run experience," "empty states," "onboarding checklist," "aha moment," or "new user experience." For signup/registration optimization, see signup-flow-cro. For ongoing email sequences, see email-sequence.
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Use when a Head of People Ops, BizOps lead, or Internal Communications owner needs to draft and sequence an internal-only change-management communication — a re-org announcement, a tool rollout, a policy change, a leadership transition, a layoff, an acquisition close, or an internal product launch — and the audience is employees (not customers). Pairs Prosci ADKAR and Kotter's 8-step change model with deterministic stdlib-only Python tools to produce a sequenced touchpoint calendar, a Kotter-compliant primary announcement, an audience-segmented FAQ, and manager cascade talking points; industry-tuned via --profile {tech-startup, scaleup, enterprise, public-company, non-profit}. Triggers on "all-hands announcement", "change comms", "rollout comms", "re-org announcement", "manager talking points", "layoff comms".
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Create professional, dark-themed SVG diagrams of any type — architecture diagrams, flowcharts, sequence diagrams, structural diagrams, mind maps, timelines, illustrative/conceptual diagrams, and more. Use this skill whenever the user asks for any kind of technical or conceptual diagram, visualization of a system, process flow, data flow, component relationship, network topology, decision tree, org chart, state machine, or any visual representation of structure/logic/process. Also trigger when the user says "画个图" "画一个架构图" "diagram" "flowchart" "sequence diagram" "draw me a ..." or uploads content and asks to visualize it. Output is always a standalone .svg file.
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Runbook for turning a new HubSpot lead in {{hubspot_list}} into a researched, personalized outbound sequence for {{projectName}}. Covers enrichment research, the outreach playbook (angles, proof points, what to avoid), sequence drafting, HubSpot logging, the daily cap, and the human approval gate before anything sends.
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Extracts protocol message flow from source code, RFCs, academic papers, pseudocode, informal prose, ProVerif (.pv), or Tamarin (.spthy) models and generates Mermaid sequenceDiagrams with cryptographic annotations. Use when diagramming a crypto protocol, visualizing a handshake or key exchange flow, extracting message flow from a spec or RFC, diagramming a ProVerif or Tamarin model, or drawing sequence diagrams for TLS, Noise, Signal, X3DH, Double Ratchet, FROST, DH, or ECDH protocols.
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Translates Mermaid sequenceDiagrams describing cryptographic protocols into ProVerif formal verification models (.pv files). Use when generating a ProVerif model, formally verifying a protocol, converting a Mermaid diagram to ProVerif, verifying protocol security properties (secrecy, authentication, forward secrecy), checking for replay attacks, or producing a .pv file from a sequence diagram.
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Generate Excalidraw diagrams from natural language descriptions. Outputs .excalidraw JSON files openable in Excalidraw. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", "generate an Excalidraw file", "draw an ER diagram", "create a sequence diagram", or "make a class diagram". Supports flowcharts, relationship diagrams, mind maps, architecture, DFD, swimlane, class, sequence, and ER diagrams. Can use icon libraries (AWS, GCP, etc.) when set up. Do NOT use for code architecture analysis (use the architecture skills), Mermaid diagram rendering (use mermaid-studio), or non-visual documentation (use docs-writer).
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Expert Mermaid diagram creation, validation, and rendering with dual-engine output (SVG/PNG/ASCII). Supports all 20+ diagram types including C4 architecture, AWS architecture-beta with service icons, flowcharts, sequence, ERD, state, class, mindmap, timeline, git graph, sankey, and more. Features code-to-diagram analysis, batch rendering, 15+ themes, and syntax validation. Use when users ask to create diagrams, visualize architecture, render mermaid files, generate ASCII diagrams, document system flows, model databases, draw AWS infrastructure, analyze code structure, or anything involving "mermaid", "diagram", "flowchart", "architecture diagram", "sequence diagram", "ERD", "C4", "ASCII diagram". Do NOT use for non-Mermaid image generation, data plotting with chart libraries, or general documentation writing.
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When the user wants to sell through social media, optimize LinkedIn for sales, build DM sequences, or convert content engagement into pipeline. Also use when the user mentions 'social selling,' 'LinkedIn selling,' 'LinkedIn DMs,' 'social prospecting,' 'LinkedIn Sales Navigator,' 'DM sequences,' 'LinkedIn outreach,' 'social pipeline,' or 'LinkedIn optimization.' This skill covers social selling strategy from profile optimization through DM-to-deal conversion. Do NOT use for technical implementation, code review, or software architecture.
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Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021). Reach for this skill to fold a sequence or complex with the AF2/AF2-Multimer evoformer, to validate designed sequences by self-consistency pLDDT, ipTM, and RMSD, or to run a quick MSA-backed prediction using the public MMseqs2 server.
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Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.
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Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring, (2) Embedding genomic windows for downstream classification, (3) Generating DNA conditioned on a prefix, (4) Scoring regulatory or coding regions across species.
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Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.
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Primary retained Python toolkit for molecular biology sequence work. Preferred for sequence manipulation, FASTA/FASTQ/GenBank parsing, Bio.Entrez, BLAST workflows, alignments, structures, and phylogenetics. For biological database evidence lookup, use bio-database-evidence. For single-cell workflows use scanpy. For direct literature REST API, use pubmed-database.
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Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
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Validate and use packed sequences and long-context training in Megatron-Bridge, including offline LLM packing, collate-time VLM packing, Energon online packing, and CP constraints.
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Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain docker run uses the slow built-in downloader.
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