「alignment」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.

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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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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.

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Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Locate CCSPlayer_MovementServices::Pawn in CS2 server.dll / libserver.so via IDA Pro MCP and emit a fresh, minimal-unique signature or offset for the local gamedata entry "CCSPlayer_MovementServices::Pawn" (symbol CCSPlayer_MovementServices_Pawn). This is a STRUCT MEMBER OFFSET (schema netvar), not a function. Resolve the CCSPlayer_MovementServices class layout via the schema/network system; the member must satisfy natural alignment. Cross-check with functions that dereference the member. Do not switch output schema: emit the structmember fields below even if the class turns out to be polymorphic - a func_*/vfunc_* payload for this symbol is rejected by canonical_symbol_yaml_bytes. Trigger: CCSPlayer_MovementServices_Pawn, CCSPlayer_MovementServices::Pawn

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Locate CCSBot::Profile in CS2 server.dll / libserver.so via IDA Pro MCP and emit a fresh, minimal-unique signature or offset for the local gamedata entry "CCSBot::Profile" (symbol CCSBot_Profile). This is a STRUCT MEMBER OFFSET (schema netvar), not a function. Resolve the CCSBot class layout via the schema/network system; the member must satisfy natural alignment. Cross-check with functions that dereference the member. Do not switch output schema: emit the structmember fields below even if the class turns out to be polymorphic - a func_*/vfunc_* payload for this symbol is rejected by canonical_symbol_yaml_bytes. Trigger: CCSBot_Profile, CCSBot::Profile

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Locate CBaseEntity::m_iTeamNum in CS2 server.dll / libserver.so via IDA Pro MCP and emit a fresh, minimal-unique signature or offset for the local gamedata entry "CBaseEntity::m_iTeamNum" (symbol CBaseEntity_m_iTeamNum). This is a STRUCT MEMBER OFFSET (schema netvar), not a function. Resolve the CBaseEntity class layout via the schema/network system; the member must satisfy natural alignment. Cross-check with functions that dereference the member. Trigger: CBaseEntity_m_iTeamNum, CBaseEntity::m_iTeamNum

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Performs a final quality pass fixing alignment, spacing, consistency, and micro-detail issues before shipping. Use when the user mentions polish, finishing touches, pre-launch review, something looks off, or wants to go from good to great.

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Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Improve layout, spacing, and visual rhythm. Fixes monotonous grids, inconsistent spacing, and weak visual hierarchy. Use when the user mentions layout feeling off, spacing issues, visual hierarchy, crowded UI, alignment problems, or wanting better composition.

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[62] VALIDATE. Final self-check before delivery. Verify goal alignment, completeness, correctness, and identify residual risks. Produces quality score (0-100) and delivery status. Use when completing any significant work, before handoff, or when you need confidence that work is ready.

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Fine-tune LLMs using reinforcement learning with TRL - SFT for instruction tuning, DPO for preference alignment, PPO/GRPO for reward optimization, and reward model training. Use when need RLHF, align model with preferences, or train from human feedback. Works with HuggingFace Transformers.

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Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

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Maxim music video — engineered for identity alignment and cultural brand affinity via Rhythm Entrainment + Mirror Neurons + Social Proof. Music videos that build cultural brand equity, not just content views.

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Maxim long-form brand story — engineered for commitment and mission alignment via StoryBrand + Hero's Journey + Emotional Arc Theory. Turns brand films into commitment mechanisms, not just awareness content.

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Maxim cinematic brand film — engineered for commitment and emotional brand alignment. Uses Hero's Journey + Peak-End Rule + Emotional Arc Theory to convert viewers into brand advocates. Use for brand films, anthem ads, founder stories, long-form brand content. Triggers on cinematic, film, brand film, anthem, dramatic, epic, Hollywood-style.

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Design meeting rhythms, metric reporting, quarterly planning, and decision-making velocity for scaling companies. Use when decisions are slow, planning is broken, the company is growing but alignment is worse, or leadership meetings consume all time without producing decisions.

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Perform a final quality pass fixing alignment, spacing, consistency, and micro-detail issues before shipping. Use when the work is functionally complete and needs finishing touches—not when the hierarchy, structure, tone, or technical foundation still need major 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。