RSV Explorer
Visualize amino acid variation across RSV clades and lineages.
Data source: Nextstrain
- Nextstrain-derived clade context
- Mutation patterns over time
- Sequence and metadata filters
Respiratory Virus Evolution Atlas
Pathogen-specific Shiny apps and reproducible pipelines for tracking amino acid variation, clade evolution, and lineage patterns across respiratory viruses and Nextclade3-supported pathogens.
Developed by Center for Applied Bioinformatics @ St. Jude Children's Research Hospital.
RSV and COVID data are downloaded from Nextstrain and processed by NextAA.
Human influenza data are downloaded from GISAID and processed by FLUAA.
Explore Amino Acid Variation
Public Shiny applications for scanning clade-aware amino acid changes across respiratory virus datasets and other Nextclade3-supported pathogens.
Pathogen-specific Explorers
Dedicated apps for RSV, SARS-CoV-2, and human Influenza datasets.
COVID Explorer
Track amino acid changes across SARS-CoV-2 clades.
Data source: Nextstrain
- Nextstrain-derived clade context
- Variant summaries by position
- Lineage and temporal views
FLU Explorer
Explore amino acid variation in human influenza viruses.
Data source: GISAID
- GISAID-derived flu sequence data
- Subtype and clade comparisons
- Research-ready visual summaries
Universal Explorer
A flexible viewer for NextAA outputs from any supported Nextstrain dataset.
AAExplorer
Universal Explorer for NextAA outputs from any Nextstrain dataset supported by Nextclade3, such as Chikungunya virus.
Data source: Nextstrain
- Universal NextAA output viewer
- Works across Nextclade3-supported pathogens
- Designed for Nextstrain-available datasets
Analysis Pipelines
Workflows for transforming global sequence resources into amino acid annotations and clade-aware explorer inputs.
NextAA Pipeline
Processes Nextstrain data for Nextclade3-supported pathogens into standardized amino acid variation outputs for AAExplorer and pathogen-specific explorers.
- Download from Nextstrain
- Standardized processing
- Amino acid annotation
- Explorer-ready exports
FLUAA Pipeline
Processes GISAID human influenza data into amino acid variation summaries for the FLU Explorer.
- Download from GISAID
- Customized flu processing
- Amino acid annotation
- Explorer-ready exports
Data Sources & Workflow
From global sequence datasets to accessible visual summaries for pathogen evolution research.
Nextstrain
NextAA
RSV, COVID & universal AAExplorer
Research Context
GISAID
FLUAA
FLU Explorer
Research Context
Built for Pathogen Evolution Research
RVE Atlas brings together public visualization apps and processing pipelines so researchers can move quickly from clade context to amino acid variation patterns across COVID, RSV, human influenza, and Nextstrain pathogens supported by Nextclade3.