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.

• Quick Start
  • Quick install
  • UShER
  • matUtils
  • matOptimize
  • RIPPLES
• Installation
  • Conda
  • Conda Local Build
  • Docker
  • Installation scripts
• UShER
  • Methodology
    • Pre-processing
    • Placement
  • Options
  • Usage
    • Display help message
    • Pre-processing global phylogeny
    • Placing new samples
  • Features
    • Branch Parsimony Score
    • Multiple parsimony-optimal placements
    • Updating multiple input trees
    • Finding sister clades
  • Converting raw sequences into VCF for UShER input
    • Generating Multiple Sequence Alignment (MSA)
    • Converting MSA to VCF
  • Presentations
  • Publications
• matUtils
  • Installation
  • The Mutation Annotated Tree (MAT) Protocol Buffer (.pb)
  • matUtils Common Options
  • summary
    • Example Usage
    • Specific Options
  • extract
    • Example Syntax and Usage
    • Specific Options
  • annotate
    • Example Syntax and Usage
    • Specific Options
  • uncertainty
    • Example Syntax and Usage
    • Options
  • introduce
    • Heuristic
    • Phylogeographic Statistics and Other Options
    • Example Syntax and Usage
    • Options
  • Publications
• matOptimize
  • Installation
  • Options
  • Presentations
• RIPPLES
  • Installation
  • Methodology
  • Options
  • Usage
  • Publications
• BTE
  • Overview
  • Installation
  • Quickstart
• Tutorials
  • Using RIPPLES to detect recombination in new sequences
    • Snakemake Workflow
  • Using Taxonium to visualize phylogenies
    • Snakemake Workflow
  • Basic matUtils Workflow
    • Snakemake Workflow
  • Example Uncertainty Workflow
  • Example Introduce Workflow
    • Snakemake Workflow
  • Calculating by-mutation RoHo with matUtils summary and Python
  • Example Amino Acid Translation Workflow
    • Snakemake Workflow
  • Interacting Directly with Protobuf Files in Python [ADVANCED USERS]

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.