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usher website  

UShER is a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny. This has emerged as an important challenge during the COVID-19 pandemic for enabling genomic contact tracing since the viral phylogeny is already very large (>2M sequences) and is expected to grow by many fold in the coming months. UShER is much faster than existing tools with similar functionality and has now also been integrated in the UCSC SARS-CoV-2 Genome Browser, which does not require UShER installation and usage know-how as described below for SARS-CoV-2 applications.

Environment Modules

Run module spider usher to find out what environment modules are available for this application.

System Variables

  • HPC_USHER_DIR - installation directory
  • HPC_USHER_BIN - executable directory


If you publish research that uses usher you have to cite it as follows:

Yatish Turakhia, Bryan Thornlow, Angie S Hinrichs, Nicola de Maio, Landen Gozashti, Robert Lanfear, David Haussler, and Russ Corbett-Detig, "Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic", Nature Genetics (2021).