UShER: Ultrafast Sample placement on Existing tRee
Place your sequences in a global phylogenetic tree

Choose your pathogen:

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:

      More example files

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

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 .