Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

SARS-CoV-2 within-host diversity and transmission

(2021) Katrina A. Lythgoe et al.   SCIENCE

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Erik Volz et al.   NATURE

Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

(2021) Delphine Planas et al.   NATURE MEDICINE

Novel Canine Coronavirus Isolated from a Hospitalized Pneumonia Patient, East Malaysia

(2021) Anastasia N Vlasova et al.   CLINICAL INFECTIOUS DISEASES

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

(2021) Emma B. Hodcroft et al.   NATURE

Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

(2021) Áine O’Toole et al.   Virus Evolution

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

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

(2020) Maciej F. Boni et al.   Nature Microbiology

The coding capacity of SARS-CoV-2

(2020) Yaara Finkel et al.   NATURE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm

(2017) Ha Minh Lam et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination

(2016) Jin Il Kim et al.   Scientific Reports

Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat

(2014) V. M. Corman et al.   JOURNAL OF VIROLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

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

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

(2011) J. Raghwani et al.   JOURNAL OF VIROLOGY

Guidelines for Identifying Homologous Recombination Events in Influenza A Virus

(2010) Maciej F. Boni et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS