Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Alarming COVID variants show vital role of genomic surveillance

(2021) David Cyranoski   NATURE

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

(2021) Tyler N. Starr et al.   SCIENCE

Covid-19: New UK variant may be linked to increased death rate, early data indicate

(2021) Gareth Iacobucci   BMJ-British Medical Journal

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

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

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

(2020) Xianding Deng et al.   SCIENCE

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Tracking virus outbreaks in the twenty-first century

(2018) Nathan D. Grubaugh et al.   Nature Microbiology

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

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Bayesian analysis of elapsed times in continuous-time Markov chains

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