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Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.

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Create and manage git worktrees for parallel coding sessions with zero dead time. Use when blocked on tests, builds, wanting to work on multiple branches, context switching, or exploring multiple approaches simultaneously.

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Coordinate the AWS DevOps Agent across multiple AgentSpaces from one Claude Code session — route questions to the right space (prod vs staging vs knowledge), query several spaces in parallel and synthesize, or compare findings across accounts. Use whenever the user has more than one AgentSpace configured, mentions multiple AWS accounts, or asks something like "check both prod and staging", "compare across accounts", or "ask the knowledge space".

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Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

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Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles.

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。

Use this skill to build a multi-element Excel dashboard — Dashboard sheet on open, multiple formula-driven KPI cards, multiple charts, sparklines, and conditional formatting — from CSV or tabular input. Trigger on: 'dashboard', 'KPI dashboard', 'analytics dashboard', 'executive dashboard', 'metrics dashboard', 'CSV to dashboard', 'data visualization'. Output is a single .xlsx. Scene-layer on officecli-xlsx: inherits every xlsx hard rule. DO NOT invoke for: a single budget tracker / one-sheet CSV-with-formatting (use xlsx), a 3-statement / DCF / LBO financial model (use financial-model), a weekly report with ≤ 1 chart and < 10 rows (use xlsx).

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Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (Bloch sphere, Wigner functions), (7) steady states and correlation functions, or (8) advanced methods (Floquet theory, HEOM, stochastic solvers). Handles both closed and open quantum systems across various domains including quantum optics, quantum computing, and condensed matter physics.

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Use when working on multiple branches simultaneously, context switching without stashing, reviewing PRs while developing, testing in isolation, or comparing implementations across branches - provides git worktree commands and workflow patterns for parallel development with multiple working directories.

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Consolidates redundant documentation while preserving all valuable content; keeps a doc set truthful after things change. Modes: (1) POST-CHANGE GOVERNANCE — when code, scripts, config, env vars, ports, paths, deployment, auth, tests, or a documented procedure changed; also "which docs are now wrong", "check docs for inconsistencies", "过时的命令/路径", "文档同步". Use it even when the user mentions only the change and never the docs — updating them is part of the change, not optional cleanup. (2) CONSOLIDATION — "clean up docs", "documentation bloat", "reduce documentation sprawl", "consolidate documentation", "too many doc files", "merge redundant docs", "merge these docs", "文档太多/太乱", multiple files covering the same topic, or documentation exceeding 500 lines across multiple files on similar topics. Finds stale copies of a fact changed in only one place, values that should never have been persisted (counts, totals, "N items", restated summaries), rival definitions that drift apart, and orphaned cross-references.

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Use this skill to build a multi-element Excel dashboard — Dashboard sheet on open, multiple formula-driven KPI cards, multiple charts, sparklines, and conditional formatting — from CSV or tabular input. Trigger on: 'dashboard', 'KPI dashboard', 'analytics dashboard', 'executive dashboard', 'metrics dashboard', 'CSV to dashboard', 'data visualization'. Output is a single .xlsx. Scene-layer on officecli-xlsx: inherits every xlsx hard rule. DO NOT invoke for: a single budget tracker / one-sheet CSV-with-formatting (use xlsx), a 3-statement / DCF / LBO financial model (use financial-model), a weekly report with ≤ 1 chart and < 10 rows (use xlsx).

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Compose Multiplatform and Jetpack Compose patterns for KMP projects — state management, navigation, theming, performance, and platform-specific UI.

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Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and accuracy tier (fast/hac/sup), requesting modified bases (5mCG_5hmCG, 6mA, m6A) at basecall time, and handling duplex, demultiplexing, trimming, and HERRO read correction. Covers why the model+version is an irreversible analysis decision, why methylation cannot be recovered later, and why downstream polish/variant models must match the basecaller. Use when converting POD5/FAST5 to reads, picking a Dorado model for R9/R10 or RNA004, enabling methylation calling, basecalling duplex, demultiplexing barcoded runs, or correcting reads for assembly.

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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.

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Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-based multiple imputation (J2R, CR, CIR, LMCF per Carpenter-Roger 2013), Permutt delta-adjustment / tipping-point analysis, pattern-mixture identifying restrictions (CCMV, NCMV, ACMV), and the Cro vs Bartlett variance debate. Use when handling missing primary or secondary endpoint data in regulatory submissions following NRC 2010 and ICH E9(R1).

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Compare several Japanese NLP libraries, models, or datasets for a keyword (a specific tool name, or a function/task like '形態素解析') across a handful of criteria chosen for that comparison, rendered as a ○/△/✕ table. Use when the user wants a side-by-side comparison of multiple Japanese NLP tools/libraries/datasets, not just the single best one. Trigger phrases include 'X と Y と Z を比較して', '形態素解析ライブラリを比較', 'MeCab と Sudachi どっちがいい', 'どのツールを使うべき', 'compare japanese tokenizers', 'mecab vs sudachi vs janome', 'which embedding model should I use', '日本語NERライブラリの比較表', 'pros and cons of japanese OCR tools'. For a single ranked list use search; for alternatives to one specific tool (or contribution candidates) without a multi-axis table, use discover.

Manage multiple Kubernetes clusters, switch contexts, and perform cross-cluster operations. Use when working with multiple clusters, comparing environments, or managing cluster lifecycle.

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Generate, evaluate, and narrow brand concepts during early ideation including positioning territories, naming candidates, mood directions, and narrative angles. Use this skill whenever the user is in the early phase of brand creation, exploring brand directions, brainstorming names, building moodboards, generating positioning options, or trying to choose between multiple brand directions. Triggers on brand ideation, brand concept, naming, brand name, name candidates, positioning, brand positioning, mood board, brand directions, exploring brands, early brand work, brand exploration, brand brainstorm, brand options. Also triggers when the user has multiple half-formed brand ideas and needs help converging on one, even if they do not say 'ideation' explicitly.

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How to read experiment results without fooling yourself. Confidence intervals, p-values, multiple testing, sequential testing, CUPED, heterogeneous treatment effects, ratio metrics, network effects, dashboard reconciliation, and the interpretation failures that produce confidently wrong shipping decisions. Use this skill whenever the user is reading a finished experiment result panel and about to make a ship, kill, or iterate decision, or when an experiment number does not match the dashboard number. Triggers on read experiment results, result panel, ship or kill decision, p-value, confidence interval, statistical significance, multiple testing, peeking, sequential testing, CUPED, variance reduction, heterogeneous treatment effects, ratio metric, network effects, inconclusive test, experiment versus dashboard mismatch. Use `experiment-design` instead when the test has not run yet and the question is hypothesis, sample size, duration, or what to test.

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Automatically evaluate and compare multiple AI models or agents without pre-existing test data. Generates test queries from a task description, collects responses from all target endpoints, auto-generates evaluation rubrics, runs pairwise comparisons via a judge model, and produces win-rate rankings with reports and charts. Supports checkpoint resume, incremental endpoint addition, and judge model hot-swap. Use when the user asks to compare, benchmark, or rank multiple models or agents on a custom task, or run an arena-style evaluation.

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