「reconstruction」の検索結果

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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。

Reconstruct workflow behind a past coding-agent artifact using local ax sessions/commits/skills/tool traces. Use when asked how X was built.

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。

Conduct multi-round deep research on any GitHub Repo. Use when users request comprehensive analysis, timeline reconstruction, competitive analysis, or in-depth investigation of GitHub. Produces structured markdown reports with executive summaries, chronological timelines, metrics analysis, and Mermaid diagrams. Triggers on Github repository URL or open source projects.

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。

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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。

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。

Conduct multi-round deep research on any GitHub Repo. Use when users request comprehensive analysis, timeline reconstruction, competitive analysis, or in-depth investigation of GitHub. Produces structured markdown reports with executive summaries, chronological timelines, metrics analysis, and Mermaid diagrams. Triggers on Github repository URL or open source projects.

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。

Leverages Splunk Enterprise Security and SPL (Search Processing Language) to investigate security incidents through log correlation, timeline reconstruction, and anomaly detection. Covers Windows event logs, firewall logs, proxy logs, and authentication data analysis. Activates for requests involving Splunk investigation, SPL queries, SIEM log analysis, security event correlation, or log-based incident investigation.

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。

Build collaborative forensic incident timelines using Timesketch to ingest, normalize, and analyze multi-source event data for attack chain reconstruction and investigation documentation.

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。

Parses and analyzes the Windows Amcache.hve registry hive to extract evidence of program execution, application installation, and driver loading for digital forensics investigations. Uses Eric Zimmerman's AmcacheParser and Timeline Explorer for artifact extraction, SHA-1 hash correlation with threat intel, and timeline reconstruction. Activates for requests involving Amcache forensics, program execution evidence, Windows artifact analysis, or application compatibility cache investigation.

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。

Reverse engineer Go-compiled malware using Ghidra with specialized scripts for function recovery, string extraction, and type reconstruction in stripped Go binaries.

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。

Uses the Linux Audit framework (auditd) with ausearch and aureport utilities to detect intrusion attempts, unauthorized access, privilege escalation, and suspicious system activity. Covers audit rule configuration, log querying, timeline reconstruction, and integration with SIEM platforms. Activates for requests involving auditd analysis, Linux audit log investigation, ausearch queries, aureport summaries, or host-based intrusion detection on Linux.

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。

LoRaWAN and sub-GHz (433 / 868 / 915 MHz) attack methodology — LoRaWAN ABP/OTAA join attack, network/session key reuse, frame counter replay, downlink injection on TTN/Helium-style networks, sub-GHz protocol replay (KeeLoq garage doors, fixed-code remotes, TPMS spoofing, smart plug telemetry), HackRF / RTL-SDR / Flipper Zero workflows, signal analysis with Inspectrum / Universal Radio Hacker, and reconstruction of proprietary packet formats. Use for LoRaWAN deployments (smart cities, asset tracking, industrial telemetry), or any wireless device using the unlicensed 433/868/915 MHz bands (garage openers, doorbells, IoT sensors, RC equipment).

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。

Offensive methodology for attacking GraphQL APIs during penetration tests and bug bounty engagements. Covers the full attack lifecycle: endpoint discovery, introspection abuse and blind schema reconstruction when introspection is disabled, authentication and authorization bypass through Relay node IDs and nested object traversal, injection via variables and directives, query batching for brute force and OTP bypass, denial of service through depth bombs and alias amplification, WebSocket subscription hijacking, information disclosure through verbose errors and field suggestion oracles, and file upload abuse via the multipart GraphQL specification. Includes tool-specific guidance for InQL, graphql-cop, CrackQL, BatchQL, Altair, GraphQL Voyager, and clairvoyance. Trigger on: GraphQL, graphql, introspection query, batching attack, query depth, GraphQL injection, GraphQL IDOR, field suggestion, GraphQL auth bypass, GraphQL DoS, GraphQL security, graphql-cop, InQL, CrackQL, BatchQL, Relay node, alias amplificat...

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。

Social engineering attack techniques beyond email phishing for authorized red team and physical penetration testing engagements. Covers pretexting methodology (persona creation, authority and urgency psychological triggers, rapport building), vishing (voice phishing via caller ID spoofing, IVR system exploitation, VoIP infrastructure setup with Twilio/Asterisk), smishing (SMS-based phishing, carrier gateway abuse, short code impersonation), physical social engineering (tailgating and piggybacking, RFID badge cloning with Proxmark3, lock picking and bypass, dumpster diving for sensitive documents), USB drop attacks (Rubber Ducky keystroke injection, Bash Bunny multi-vector payloads, O.MG cable covert implants, BadUSB firmware attacks), watering hole attack planning and execution, and OSINT-driven targeting (LinkedIn harvesting, organizational chart reconstruction, employee pattern analysis). Integrates with the Social Engineering Toolkit for attack automation, Proxmark3 for RFID/NFC cloning, USB Rubber Duc...

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。

Structured OSINT methodology framework: target definition, source selection, collection workflows, data correlation, timeline reconstruction, and reporting. Use to guide systematic OSINT campaigns or teach OSINT methodology.

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。

Advanced CV for infrastructure inspection including forest fire detection, wildfire precondition assessment, roof inspection, hail damage analysis, thermal imaging, and 3D Gaussian Splatting reconstruction. Expert in multi-modal detection, insurance risk modeling, and reinsurance data pipelines. Activate on "fire detection", "wildfire risk", "roof inspection", "hail damage", "thermal analysis", "Gaussian Splatting", "3DGS", "insurance inspection", "defensible space", "property assessment", "catastrophe modeling", "NDVI", "fuel load". NOT for general drone flight control, SLAM, path planning, or sensor fusion (use drone-cv-expert), GPU shader development (use metal-shader-expert), or generic object detection without inspection context (use clip-aware-embeddings).

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。

Conduct Critical Decision Method (CDM) interviews to elicit expert reasoning strategies (L3 knowledge) from practitioners about specific challenging past incidents. Use when capturing expertise for skill development, preserving knowledge before practitioner departure, building post-incident learning artifacts, or investigating decisions in complex sociotechnical systems. Outputs structured incident reconstructions with cues, decisions, alternatives considered, and counterfactual analysis suitable for distillation into skills or training material.

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。