Create Phylogenetic Tree of SARS CoV 2 by UShER

There are nearly 14 million viral genome sequences right now in the GISAID EpiCoV ™ database. It is not likely to infer the phylogenetic relationships for such a huge dataset by traditional maximum likelyhood or Bayesian methods in a shor time period. The UShER package was developed to generate ultra-large phylogenetic tree of SARS-CoV-2 genomes. The algorithm of the UShER program is to place new samples onto an existing phylogeny using maximum parsimony method. It is able to place given SARS-CoV-2 genome sequences into the GISAID global phylogeny in a couple of hours. This program is …