'trees' 검색 결과

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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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.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

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

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Use when: User wants to run Archon workflows, CREATE workflows or commands, set up Archon, or manage Archon configuration. Triggers (run): "use archon to", "run archon", "archon workflow", "use archon for", "have archon", "let archon", "ask archon to". Triggers (create): "create a workflow", "write a workflow", "make a command", "author a workflow", "new workflow", "new command", "archon workflow yaml". Triggers (setup): "set up archon", "install archon", "how to use archon", "configure archon", "archon setup", "get started with archon". Triggers (config): "change my archon config", "modify archon config", "archon config", "change archon settings", "update my config", "help me change my config", "edit archon config", "archon configuration". Triggers (init): "initialize archon", "set up .archon", "archon init", "add archon to repo". Capability: Runs AI workflows in isolated git worktrees for parallel development. Also: Creates and manages workflow YAML files, command files, and configuration. NOT for: Direct Claude Code work - only for delegating to Archon CLI.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

The PRIMARY development workflow for the Archon project (remote-coding-agent). Use this skill instead of any PRP skills when working on Archon code. Routes to 10 specialized cookbooks based on what the user is trying to do: RESEARCH — "how does the orchestrator work?", "where is session state defined?", "trace the workflow execution flow", "what is IWorkflowStore?" INVESTIGATE — "should we use Drizzle or Prisma?", "what's the best way to add WebSockets?", "can we migrate to Turso?", "how do other projects handle rate limiting?" PRD — "write a PRD for dark mode", "spec out the notification feature", "product requirements for webhook retry" PLAN — "plan the auth refactor", "design the caching layer", "create an implementation plan for #42" IMPLEMENT — "implement the plan", "execute .claude/archon/plans/auth.plan.md", "build the feature from the plan", "code this up" REVIEW — "review PR #123", "review my changes", "code review the diff" DEBUG — "debug the failing test", "why is streaming broken?", "root cause analysis on the timeout issue" COMMIT — "commit these changes", "commit the auth refactor" PR — "create a PR", "open a pull request for this branch" ISSUE — "report this to gh", "create a gh issue", "log it in github", "file a bug for this", "create a feature request" This skill triggers on ANY development task: researching, investigating, planning, building, reviewing, debugging, committing, or shipping code. NOT for: Running Archon CLI workflows in worktrees (use /archon instead).

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Launch, inspect, and tear down autonomous phase fleets in isolated Git worktrees, on the Codex or the Claude runtime. Use when approved Flow phase slugs should run in parallel, when fleet status is requested, or when a fleet member must be stopped or explicitly merged.

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Safely clean up local branches whose tracked remote branch is gone. Use when you want to review stale branches and associated worktrees after remote branches or PRs are deleted.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Designs Rust command-line interfaces that are reliable for agents, scripts, and humans. Use when building or reviewing Rust binaries, clap command trees, diagnostics commands, codegen tools, or automation-facing workflows.

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Clean up git branches marked as [gone] (deleted on remote but still exist locally). Use when you want to prune stale local branches, remove worktrees for deleted branches, or clean up after PR merges.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Idiomatic Go - package and interface design, error wrapping, table-driven tests, generics, the modern standard library (slices/maps/cmp/errors.Join), current syntax, and logging discipline. Use when writing, reviewing, or refactoring any Go code, especially code drifting toward Java/Spring shapes (deep layer trees, generic repositories, heavy frameworks) - even if the user never says "idiomatic". Distilled from spf13/go-skills and adapted to this repo.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Cleans up local git branches marked as [gone] (deleted on the remote but still present locally), including removing any associated worktrees. Use when the user says "prune branches", "clean up gone branches", "/prune-branches", or asks to delete stale local branches whose remotes are gone.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

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

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

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.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Naturalistic causal reasoning for failures and disputed attribution. Use when postmortems or root-cause debates need reframing. NOT for causal inference, fault trees, or fully observed failures.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Naturalistic causal reasoning for failures and disputed attribution. Use when postmortems or root-cause debates need reframing. NOT for causal inference, fault trees, or fully observed failures.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

The standing order for local git state in every AI Matrx repo — zero worktrees, zero local branches, zero dirty files, zero open PRs, everything merged to origin/main, and no code ever lost. Use when you find a worktree, a local branch, a stale checkout, an unpushed commit, or a dirty tree in any repo under /Users/armanisadeghi/code, when asked to "clean up", "unify", "merge everything", or when you are tempted to create a worktree or branch. Works without any access to Arman.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Manage git worktrees for isolated development. Use when creating isolated workspaces, managing parallel development, handling worktree lifecycle, or merging completed work.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

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

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Analyze V8/Chrome CPU profiles (.cpuprofile) and DevTools trace files (Trace-*.json). Use when: profiling performance, investigating slow functions, comparing code paths, finding bottlenecks, analyzing timeToRequest, understanding call trees from sampling profiler data, analyzing layout/paint/rendering, investigating user timing marks.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

5 proven agent skill design patterns (Tool Wrapper, Generator, Reviewer, Inversion, Pipeline) from Google's ADK. Build reliable, composable skills with templates, decision trees, and composition guides. Stop cramming logic into prompts—use structured patterns instead.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Write idiomatic Elixir code with OTP patterns, supervision trees, and Phoenix LiveView. Masters concurrency, fault tolerance, and distributed systems. Use PROACTIVELY for Elixir refactoring, OTP design, or complex BEAM optimizations.

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Renders rich console output. Spectre.Console tables, trees, progress, prompts, live displays.

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Create safe, deterministic git worktrees for large or risky workstreams using the repository-owned runtime helper and Windows-safe defaults.

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