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Choose your pathogen: SARS-CoV-2 Dengue (types 1 - 4) H5N1 2024 outbreak: concatenated segments Influenza A RSV-A RSV-A (RGCC Nov. 2023) RSV-B RSV-B (RGCC Nov. 2023) hMPXV
Select your FASTA, VCF or list of sequence names/IDs:
or paste in sequence names/IDs:
Phylogenetic tree version: 8,260,461 genomes from GenBank, COG-UK and CNCB (2024-12-01); sarscov2phylo 13-11-20 tree with newer sequences added by UShER 16,727,360 genomes from GISAID, GenBank, COG-UK and CNCB (2024-12-01); sarscov2phylo 13-11-20 tree with newer sequences added by UShER
Number of samples per subtree showing sample placement:
Prevent subtree Auspice JSON files from expiring after two days:
More example files
Upload your SARS-CoV-2 sequence (FASTA or VCF file) to find the most similar complete, high-coverage samples from GISAID or from public sequence databases (INSDC: GenBank/ENA/DDBJ accessed using NCBI Virus, COG-UK and the China National Center for Bioinformation), and your sequence's placement in the phylogenetic tree generated by the sarscov2phylo pipeline. Placement is performed by Ultrafast Sample placement on Existing tRee (UShER) (Turakhia et al.). UShER also generates local subtrees to show samples in the context of the most closely related sequences. The subtrees can be visualized as Genome Browser custom tracks and/or using Nextstrain's interactive display which supports drag-and-drop of local metadata that remains on your computer. If the subtree size is set to 500 or smaller, then subtrees can also be visualized in MicrobeTrace, a network visualization tool that integrates and overlays genomic, laboratory, and epidemiologic data and offers multiple visualization options of your combined data.
GISAID data displayed in the Genome Browser are subject to GISAID's Terms and Conditions. SARS-CoV-2 genome sequences and metadata are available for download from GISAID EpiCoV™.
COVID-19 Pandemic Resources at UCSC
We do not store your information (aside from the information necessary to display results) and will not share it with others unless you choose to share your Genome Browser view.
In order to enable rapid progress in pandemic research and genomic contact tracing, please share your sequences by submitting them to an INSDC member institution (NCBI, EMBL-EBI or DDBJ) and GISAID .
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