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 on the sidebar, or click here for a quick tutorial on getting started.

UShER

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

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

matOptimize

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

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.

BTE

BTE is a separately packaged Cython API that wraps the highly optimized library underlying these other tools, exposing them for use in Python. Information about its usage can be found here and at its repository.