「evolution」の検索結果

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.

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。

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.

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。

Large-scale data migrations with validation, rollback, and zero-downtime strategies. Activate on: data migration, database migration, zero-downtime migration, dual-write, backfill, cutover, data validation, schema migration. NOT for: schema evolution in streams (use schema-evolution-manager), API versioning (use api-versioning-backward-compatibility).

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。

Great Expectations, dbt tests, anomaly detection, and data contracts for data quality. Activate on: data quality, data validation, Great Expectations, data contract, anomaly detection, SLA, freshness check, schema validation. NOT for: dbt model structure (use dbt-analytics-engineer), schema evolution (use schema-evolution-manager).

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。

API migration strategies, deprecation workflows, and header/URL/content versioning. Activate on: API versioning, backward compatibility, deprecation, breaking change, API migration, v1 v2, sunset header. NOT for: schema evolution in data (use schema-evolution-manager), gateway routing (use api-gateway-reverse-proxy-expert).

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。

Expert-level stellar physics covering stellar structure and evolution, nucleosynthesis, stellar atmospheres, variable stars, binary systems, and stellar populations.

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。

Solves complex, open-ended problems using an evolutionary search mechanism inspired by genetic algorithms. Generates a diverse population of candidate answers, scores them against a rubric, then iteratively applies selection, crossover, and mutation to breed progressively better solutions. Use this skill whenever the user wants to explore a solution space deeply, asks for the "best" answer to a subjective or multi-dimensional problem, wants to evaluate competing approaches and distill the strongest, or uses any of these triggers: "evolutionary search", "genetic algorithm", "evolve an answer", "breed solutions", "population-based search", or phrases like "give me multiple approaches and refine the best one". Also trigger when the problem is complex, open-ended, or has no obvious single correct answer and the user wants a high-quality, well-explored result, not just a quick response.

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。

Wardley Mapping for strategic positioning — map your value chain from customer need to underlying components, plot where each component sits on the evolution curve (novel to commodity), and spot the strategic plays that movement creates. Use this skill when someone wants to understand where their industry is heading, whether they're building things they should be buying, where competitors are vulnerable, what's about to become commoditised, or why their competitive advantage is eroding. Triggers on questions about build-vs-buy, component evolution, value chain analysis, commoditisation risk, or strategic positioning relative to market movement. Three modes — full diagnostic (build a map from scratch), review (update positions and reassess), and alert triggers (set tripwires for when components move). Based on practice by Eterdis (eterdis.com).

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。

METAINFORMANT rules for directory src/metainformant/math/evolutionary_dynamics. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

Evolutionary file renaming with wrapper files. Enables renames without hard breaks — references are organically updated through usage.

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。

Evolutionary file renaming with wrapper files, plus the terse MOVED-stub standard for whole folder/file moves. Enables renames without hard breaks — references are organically updated through usage.

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。

Cascade approved evolution changes through downstream layers, assess impact, run consistency checks, and write evolution audit record

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。

Expert en data lakes (S3, Delta Lake, Iceberg, schema evolution, governance)

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。

Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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。

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.

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。

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.

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。

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.

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。

Seed minimal agent harness v0 — manifest, eval checks stub, governance. AUTO-INVOKED after project-setup or retroactive-project-setup when docs/harness/manifest.json is missing. Also triggers on: generate harness, scaffold agents, agent bootstrap, first time agents in this repo, new project agent setup, set up agent harness, agent onboarding files, missing agent configuration, agent instructions setup, make agents read project rules, agent reliability setup, agents not configured. Pairs with project-setup. Evolution is harness-evolution.

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。

Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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。

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.

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。

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.

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。

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.

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。

Evolve prompts/regex/SQL/code with Imbue's evolution loop.

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。

Plans safe API evolution with versioning strategies, client migration guides, deprecation timelines, and backward compatibility considerations. Use for "API versioning", "deprecation planning", "API evolution", or "breaking changes".

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。