UShER: Ultrafast Sample placement on Existing tRee

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 (NCBI Virus / GenBank, 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.

The CDC COVID-19 Genomic Epidemiology Toolkit now includes a training module for UShER! Module 3.3 includes a video, slides (PDF), and links to more resources.

Note: Please do not upload any files that contain Protected Health Information (PHI) to UCSC. 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 SARS-CoV-2 research and genomic contact tracing, please share your SARS-CoV-2 sequences by submitting them to an INSDC member institution (NCBI, EMBL-EBI or DDBJ) and GISAID.

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

or paste in sequence names/IDs:

Phylogenetic tree version:

Number of samples per subtree showing sample placement:

If you don't have a local file, you can try an example:

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™.