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.
- Quick Start
- Converting raw sequences into VCF for UShER input
- The Mutation Annotated Tree (MAT) Protocol Buffer (.pb)
- matUtils Common Options
- Using RIPPLES to detect recombination in new sequences
- Using Taxonium to visualize phylogenies
- Basic matUtils Workflow
- Example Uncertainty Workflow
- Example Introduce Workflow
- Calculating by-mutation RoHo with matUtils summary and Python
- Example Amino Acid Translation Workflow
- Interacting Directly with Protobuf Files in Python [ADVANCED USERS]
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.
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.