Choose your pathogen: SARS-CoV-2 Dengue (types 1 - 4) H5N1 B3.13 (cattle) 2024 outbreak: concatenated segments H5N1 D1.1 2024 outbreak: concatenated segments Influenza A M. tuberculosis H37Rv Measles Mpox RSV RSV (reference: RGCC reconstructed root)
Can't find the pathogen you're looking for? Try placing your sequences with Taxonium! (backed by viral_usher)

Select your FASTA, VCF or list of sequence names/IDs:

or paste in sequence names/IDs:

Phylogenetic tree version: 8,460,947 genomes from GenBank, COG-UK and CNCB (2026-09-09); sarscov2phylo 13-11-20 tree with newer sequences added by UShER 258,904 recent genomes from GISAID, GenBank, COG-UK and CNCB (2026-09-09); sarscov2phylo 13-11-20 tree with newer sequences added by UShER 17,316,857 genomes from GISAID, GenBank, COG-UK and CNCB (2026-09-09); 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:

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More information

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

Download public tree files

Tree and metadata files in various formats can be downloaded from https://hgdownload.gi.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/.

Privacy and sharing

Please do not upload Protected Health Information (PHI).

If even virus sequence files must remain local on your computer, then you can try ShUShER which runs entirely in your web browser so that no files leave your computer.

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 .

Tutorial

Slides for tutorial

More tutorials from CDC COVID-19 Genomic Epidemiology Toolkit