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yatisht committed Nov 29, 2020
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**NEW: We will now be sharing and updating UShER's pre-processed mutation-annotated tree object for public SARS-CoV-2 sequences here: https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/**

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 this pandemic for enabling *genomic contact tracing* since the viral phylogeny is already very large (>50K sequences, see https://github.com/roblanf/sarscov2phylo/releases) and is expected to grow by many fold in the coming months.
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 this pandemic for enabling *genomic contact tracing* since the viral phylogeny is already very large (>100K sequences, see https://github.com/roblanf/sarscov2phylo/releases) 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](https://genome.ucsc.edu/cgi-bin/hgPhyloPlace), which does not require UShER installation and usage know-how as described below for SARS-CoV-2 applications. Please follow the steps below if you wish to use UShER in a standalone fashion.

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