Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

(2021) Yatish Turakhia et al.   NATURE GENETICS

SARS-CoV-2 variants, spike mutations and immune escape

(2021) William T. Harvey et al.   NATURE REVIEWS MICROBIOLOGY

Outbreak of SARS-CoV-2 Infections, Including COVID-19 Vaccine Breakthrough Infections, Associated with Large Public Gatherings — Barnstable County, Massachusetts, July 2021

(2021) Catherine M. Brown et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

(2020) Qianqian Li et al.   CELL

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Genetic bottlenecks in intraspecies virus transmission

(2018) John T McCrone et al.   Current Opinion in Virology

outbreaker2: a modular platform for outbreak reconstruction

(2018) Finlay Campbell et al.   BMC BIOINFORMATICS

Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus

(2017) Ashley Sobel Leonard et al.   JOURNAL OF VIROLOGY

Genomic Analysis of Viral Outbreaks

(2016) Shirlee Wohl et al.   Annual Review of Virology

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics

(2013) Anne Cori et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION