COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

(2021) Lewis F. Buss et al.   SCIENCE

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

(2021) Wilfredo F. Garcia-Beltran et al.   CELL

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

(2021) Ester C Sabino et al.   LANCET

Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

(2021) Houriiyah Tegally et al.   NATURE

SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

(2021) Markus Hoffmann et al.   CELL

Antibody evasion by the P.1 strain of SARS-CoV-2

(2021) Wanwisa Dejnirattisai et al.   CELL

Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization

(2021) Pengfei Wang et al.   Cell Host & Microbe

The emerging plasticity of SARS-CoV-2

(2021) Kevin D. McCormick et al.   SCIENCE

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

(2021) Nuno R. Faria et al.   SCIENCE

Evolution and epidemic spread of SARS-CoV-2 in Brazil

(2020) Darlan S. Candido et al.   SCIENCE

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

(2020) Daniele Mercatelli et al.   Frontiers in Microbiology

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

(2020) Andrew Rambaut et al.   Nature Microbiology

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

(2019) Sohta A Ishikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen 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 gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

(2011) F. Bielejec et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Bayesian analysis of elapsed times in continuous-time Markov chains

(2010) Marco A. R. Ferreira et al.   CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Many-core algorithms for statistical phylogenetics

(2009) M. A. Suchard 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