UShER (Ultrafast Sample placement on Existing tRees) describes a new method for placing new genome sequences onto an existing phylogeny of the SARS-CoV-2 virus that is orders of magnitude faster than existing approaches and produces highly accurate results. For details, consult the paper

https://www.nature.com/articles/s41588-021-00862-7

For installation instructions and other details about the software, see 

https://usher-wiki.readthedocs.io/en/latest/UShER.html