Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

(2022) Filipe Zimmer Dezordi et al.   Viruses-Basel

Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil

(2022) Felipe Gomes Naveca et al.   Microbiology Spectrum

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

(2021) Carolina M. Voloch et al.   JOURNAL OF VIROLOGY

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

(2021) Ester C Sabino et al.   LANCET

Impact of domestic travel restrictions on transmission of COVID-19 infection using public transportation network approach

(2021) Yayoi Murano et al.   Scientific Reports

Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil

(2021) Paola Cristina Resende et al.   Frontiers in Microbiology

Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate, February 2021, Rio Grande do Sul, Southern Brazil

(2021) Andreza Francisco Martins et al.   Eurosurveillance

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

(2021) Felipe Gomes Naveca et al.   NATURE MEDICINE

The impact of super-spreader cities, highways, and intensive care availability in the early stages of the COVID-19 epidemic in Brazil

(2021) Miguel A. L. Nicolelis et al.   Scientific Reports

Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil

(2021) Stephane Tosta et al.   PLoS Neglected Tropical Diseases

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

(2021) Alessandra P. Lamarca et al.   PLoS Neglected Tropical Diseases

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

(2020) Darlan S. Candido et al.   SCIENCE

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

(2020) Andrew Rambaut et al.   Nature Microbiology

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

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   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

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

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

(2010) B. Shapiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

(2009) J. D. O'Brien et al.   MOLECULAR BIOLOGY AND EVOLUTION