UShER Wiki

Welcome to the manual for UShER package, that includes SARS-CoV-2 Phylogenetics tools UShER, matUtils, matOptimize, RIPPLES, strain_phylogenetics, and others. Please see the table of contents below or on the sidebar, or click here for a quick tutorial on getting started.



UShER is a program for rapid, accurate placement of samples to existing phylogenies. Information on installation, usage, and features can be found here. Our manuscript about UShER can be found here.


matUtils is a toolkit for querying, interpreting and manipulating the mutation-annotated trees (MATs). Information on its usage can be found here.


matOptimize is a program to rapidly and effectively optimize a mutation-annotated tree (MAT) for parsimony using subtree pruning and regrafting (SPR) moves within a user-defined radius. Information on its usage can be found here.


RIPPLES is a program that uses a phylogenomic technique to rapidly and sensitively detect recombinant nodes and their ancestors in a mutation-annotated tree (MAT). Information on its usage can be found here.