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doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a s

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Prepare training datasets for large language models with GPU-assisted cleaning. Covers duplicate removal, quality filtering, and personal information redaction, with workflows for text, images, video, and audio using NeMo Curator.

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• Clean web data for model training
• Remove exact and near duplicates from large text collections
• Redact personal information from training text

Prepare training datasets for large language models with GPU-assisted cleaning. Covers duplicate removal, quality filtering, and personal information redaction, with workflows for text, images, video, and audio using NeMo Curator.

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• Clean web data for model training
• Remove exact and near duplicates from large text collections
• Redact personal information from training text

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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MEMO-ONLY prior-work overlap advisory: surfaces the two ADVISORY taxonomy signals neither a tool nor a model can decide from the paper alone — ADV-TRIVIAL-COMBINATION (standard A+B+C / 缝合 stapling) and ADV-DUPLICATE-PUBLICATION (repackaged / duplicate submission). The executor RETRIEVES candidate prior work (DBLP fuzzy-title + boolean · WebSearch · WebFetch) from the paper's own title + contribution spans in the evidence ledger; TWO fresh cross-model codex reviewers (one per axis) LAY OUT the overlap side-by-side against each anchored contribution claim. It NEVER rules 'trivial' or 'duplicate' (that is a human judgment) and absence of a match is NOT evidence of originality. Emits novelty-duplication-advisory.memo.md + an info-only findings mirror; carries NO verdict weight — tools/adjudicate_findings.py lists it in ZERO_WEIGHT_SKILLS and caps it at info. Detect-only. Adapted from ARIS novelty-check, reframed from 'is MY idea novel' to 'here is the overlap a reviewer should weigh'. Triggers: "novelty advisory", "duplication check", "prior-work overlap", "is this stapling", "缝合", "查重", "重复发表", "duplicate submission".

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Drive a PR to a green quality gate and keep it there. Loops on SonarCloud for the project's targets, no new issues, no duplication on new code, and coverage on new logic as close to 100% as the code allows, then watches the PR checks until every one passes. Use when a quality gate blocks a merge, when coverage or duplication has to come up, or before asking for review. Triggers - "fix the sonar issues", "quality gate", "get coverage up", "zero duplication", "loop until CI is green", "watch the checks".

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Build AI data deduplication systems. TRIGGERS - Use when user needs help with ai-deduplication related tasks.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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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.

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Build AI data deduplication systems. TRIGGERS - Use when user needs help with ai-deduplication related tasks.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DTL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DTL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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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.

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在保持行为不变的前提下，整理深层条件分支、长函数、重复逻辑和含糊命名。先检查现有规范与测试，再以可读性为标准逐步修改。

• 改善已正常运行功能的代码可读性
• 处理代码审查指出的复杂逻辑
• 整理深层条件分支和长函数

Find prospects by role, industry, company size, and location, then add approved contacts to an Apollo sequence, a series of outreach emails. The workflow enriches details, creates contacts with deduplication, and reports enrollment results.

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• Finding prospects by role and company criteria
• Adding a batch of contacts to an Apollo sequence
• Loading another batch into an existing sequence

Review recent code changes for duplication, maintainability, and wasted work, then apply straightforward improvements. The workflow combines three parallel reviews, prioritizes small, low-risk fixes, and checks the edited code with relevant tests or project checks.

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• Cleaning up code after implementation
• Polishing changes before opening a pull request
• Reducing duplication in recent changes

Convert Snowflake dbt SQL models to BigQuery through a bulk migration workflow. Preserve Jinja template logic while adapting configuration, explicit type conversions, JSON access, and deduplication patterns, with translated files saved in their directory structure.

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• Migrating Snowflake dbt models to BigQuery in bulk
• Preserving dbt references and incremental processing logic
• Adapting JSON, array, and STRUCT access during migration

Review code changes for correctness, readable names, clear interfaces, and design problems. Examine duplication, hidden assumptions, and unnecessary abstractions, then report actionable findings with file locations, explanations, and concrete suggestions for fixes.

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• Review pull request changes
• Check names and function interfaces
• Find duplication and unclear responsibilities

Audit server-side advertising measurement by comparing browser and server events, checking duplicate handling, consent, and data quality. Reconcile platform diagnostics with source logs and business conversions, then return prioritized findings, owners, and verification steps.

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• Investigate missing or duplicated conversion events
• Compare browser and server event data
• Review consent and data handling before transmission

Analyze a monolithic codebase before splitting it into modules or services. The skill inventories components, examines duplication, hierarchy, and dependencies, then proposes groupings aligned with business domains, with optional checks against business terminology and boundaries.

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• Assessing component sizes before splitting a monolith
• Finding duplicated business logic across modules
• Reviewing module hierarchy and dependencies

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.

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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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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.

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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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