Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Genetic Variants of SARS-CoV-2—What Do They Mean?

(2021) Adam S. Lauring et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

(2021) Summer E. Galloway et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Public health actions to control new SARS-CoV-2 variants

(2021) Nathan D. Grubaugh et al.   CELL

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Nicholas G. Davies et al.   SCIENCE

Covid-19: The E484K mutation and the risks it poses

(2021) Jacqui Wise   BMJ-British Medical Journal

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

(2020) Joseph R. Fauver et al.   CELL

Introductions and early spread of SARS-CoV-2 in the New York City area

(2020) Ana S. Gonzalez-Reiche et al.   SCIENCE

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region

(2020) Matthew T Maurano et al.   GENOME RESEARCH

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology