Results for “duplication”

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

The English summary is being prepared. Showing the original description.

Improves code quality across duplication, efficiency, and architectural fit. Use when code passes tests but quality is poor or before a major release.

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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 and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Perform a comprehensive DRY (Don't Repeat Yourself) code review on a codebase. Identifies duplicated code, repeated logic, redundant patterns, and opportunities for abstraction. Use this skill whenever the user asks to review code for duplication, reduce repetition, apply DRY principles, refactor for reusability, find copy-pasted code, deduplicate logic, or audit code quality with a focus on redundancy. Also trigger when users say things like "clean up my code", "find repeated patterns", "too much boilerplate", "reduce code duplication", or "refactor for maintainability". Works on any language or framework.

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Audit server-side paid-media measurement including server-side tag management, platform conversion APIs, event taxonomy, browser/server deduplication, consent, hashing, data quality, observability, and privacy. Use for server-side tracking, sGTM, server-side tagging, Meta CAPI, TikTok Events API, event_id, deduplication, pixel debugging, first-party measurement, or conversion data loss.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

The English summary is being prepared. Showing the original description.

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

The English summary is being prepared. Showing the original description.

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 and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

The English summary is being prepared. Showing the original description.

Deploy DefectDojo as a centralized vulnerability management dashboard with scanner integrations, deduplication, metrics tracking, and Jira ticketing workflows.

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Create an Estuary derivation with custom SQLite state (internal tables) to make per-document decisions based on accumulated history — account balances, inventory levels, approval workflows, deduplication. Derivations add complexity and cost — confirm the user wants a derivation before reaching for this. Use when user says "stateful derivation", "derivation to track balance", "transformation to approve based on state", "derive an approval workflow", "deduplication derivation", or "build a stateful derivation".

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Data Quality Specialist IA — Expert en qualité des données (profiling, cleaning, déduplication, validation de schéma, Great Expectations)

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Deploy DefectDojo as a centralized vulnerability management dashboard with scanner integrations, deduplication, metrics tracking, and Jira ticketing workflows.

The English summary is being prepared. Showing the original description.

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

The English summary is being prepared. Showing the original description.

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 and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

The English summary is being prepared. Showing the original description.

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

The English summary is being prepared. Showing the original description.

GPU-accelerated data curation for LLM training. Supports text/image/video/audio. Features fuzzy deduplication (16× faster), quality filtering (30+ heuristics), semantic deduplication, PII redaction, NSFW detection. Scales across GPUs with RAPIDS. Use for preparing high-quality training datasets, cleaning web data, or deduplicating large corpora.

The English summary is being prepared. Showing the original description.

Improve code structure, readability, and maintainability without changing external behavior through systematic refactoring techniques like extracting functions, removing duplication, simplifying conditionals, and applying design patterns. Use when reducing technical debt, extracting functions or classes, removing code duplication, simplifying complex conditionals, renaming for clarity, applying design patterns, improving code organization, reducing coupling, increasing cohesion, or maintaining test coverage during structural improvements.

The English summary is being prepared. Showing the original description.

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 and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

The English summary is being prepared. Showing the original description.

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

The English summary is being prepared. Showing the original description.

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

The English summary is being prepared. Showing the original description.

Deploy DefectDojo as a centralized vulnerability management dashboard with scanner integrations, deduplication, metrics tracking, and Jira ticketing workflows.

The English summary is being prepared. Showing the original description.

Create and edit documents that AI agents follow, including skills and project instructions. Organize steps and reference material, define clear completion criteria, and refine document links and wording to reduce duplication and unnecessary context.

• Creating or editing a skill document
• Organizing AGENTS.md or CLAUDE.md
• Clarifying when agents should read reference files

Apply shared coding conventions to new modules, reviews, and refactoring. Guides descriptive naming, readable structure, updates that preserve existing data, and error handling, giving teams a consistent basis for checking code quality.

• Setting coding conventions for a new project
• Reviewing code readability and maintainability
• Refactoring duplication and deeply nested logic

Design a shared notification workflow across GitHub, Linear, local hooks, desktop alerts, and existing communication tools. Classify urgency and ownership, merge duplicate events, and decide which updates need immediate attention, a digest, or a log entry.

• Consolidate GitHub, Linear, and local hook notifications
• Reduce duplicate alerts for CI failures
• Separate urgent alerts from digest updates