A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

Alarming COVID variants show vital role of genomic surveillance

(2021) David Cyranoski   NATURE

Want to track pandemic variants faster? Fix the bioinformatics bottleneck

(2021) Emma B. Hodcroft et al.   NATURE

Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution

(2021) A Chaillon et al.   CLINICAL INFECTIOUS DISEASES

One million coronavirus sequences: popular genome site hits mega milestone

(2021) Amy Maxmen   NATURE

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

The UCSC SARS-CoV-2 Genome Browser

(2020) Jason D. Fernandes et al.   NATURE GENETICS

Stability of SARS-CoV-2 phylogenies

(2020) Yatish Turakhia et al.   PLoS Genetics

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

(2020) Ana da Silva Filipe et al.   Nature Microbiology

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION