「lineages」の検索結果

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme churn (V3/V4/V4.1/V5.3.2/Midnight) with dropout regions, and recombinant X-prefix designation lag. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater into lineage frequencies with Freyja, tracking lineage frequencies over time, handling ARTIC primer dropouts, or running surveillance for SARS-CoV-2/influenza/Mpox/RSV/H5N1/measles.

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。

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme churn (V3/V4/V4.1/V5.3.2/Midnight) with dropout regions, and recombinant X-prefix designation lag. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater into lineage frequencies with Freyja, tracking lineage frequencies over time, handling ARTIC primer dropouts, or running surveillance for SARS-CoV-2/influenza/Mpox/RSV/H5N1/measles.

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。

Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant surveillance for SARS-CoV-2 / influenza / Mpox / RSV / H5N1 / measles.

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。

Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant surveillance for SARS-CoV-2 / influenza / Mpox / RSV / H5N1 / measles.

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。

Understand how ideas evolved over time to find old solutions for new problems and avoid repeating past failures

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。

Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks. Use when deciding bulk vs single-cell (bulk amplicon/RNA-seq -> MiXCR analyze preset -> VDJtools/immunarch depth-normalized diversity and overlap -> figures; 10x paired VDJ -> MiXCR 10x preset or Cell Ranger -> scirpy gene-expression integration, chain QC, clonotype clusters); and TCR vs BCR (TCR -> exact CDR3-nt+V/J clonotypes, VDJtools diversity is fine; BCR -> somatic hypermutation makes exact clonotypes wrong -> Immcantation distToNearest/findThreshold clonal clustering, germline reconstruction, SHM, Dowser lineages); selecting the MiXCR 4.x preset by chemistry and activating its license; downsampling to equal depth before comparing diversity or overlap; and optionally annotating antigen specificity.

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。

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for variant surveillance, Pango lineage validation, dominant submitted lineages, Nextclade assignment provenance, SARS-CoV-2, influenza/H5N1 clades, RSV, mpox, measles, dengue, or LAPIS queries. Distinguishes sequence prevalence from infection prevalence, clades from genotypes, missing calls from reference matches, and sampling changes from biological growth advantage.

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。

Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.

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, 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.

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 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.

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。

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.

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 horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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。

Understand how ideas evolved over time to find old solutions for new problems and avoid repeating past failures

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。

Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenies with fossils, choosing between strict and relaxed clock models, or estimating evolutionary rates across lineages.

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。

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.

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。

Traditional Chinese internal arts — tai chi chuan and qigong — as transmitted by classical lineages (Chen, Yang, Wu, Wu/Hao, Sun for tai chi; Ba Duan Jin, Yi Jin Jing, Liu Zi Jue, Wu Qin Xi, and other named sets for qigong) with an emphasis on alignment, rooted stance, breath-posture-mind coordination (the three harmonies), and the traditional lineage voice that Dr. Yang Jwing-Ming's YMAA line preserves. Also covers the safety boundary between traditional practice and clinical "medical qigong" claims. Use for queries about tai chi form learning, qigong set selection, internal-arts pedagogy, and the practical question of where to start.

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。

Major art movements and their historical context for art education. Covers 12 movements from the Renaissance to contemporary art, their defining characteristics, key artists, signature works, and the intellectual/social forces that produced them. Use when analyzing artworks in historical context, understanding stylistic lineages, identifying influences across periods, or connecting studio practice to art-historical precedent.

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。

Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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。

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.

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, 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.

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 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.

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。

Use the Malpedia platform and API to research malware family relationships, track variant evolution, link families to threat actors, and integrate YARA rules for detection across malware lineages.

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。