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 Taxodium 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 with MAT Protobuf in Python [ADVANCED USERS]
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.