Transmission dynamics and evolutionary history of 2019‐nCoV

Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

(2020) Xingguang Li et al.   JOURNAL OF MEDICAL VIROLOGY

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

(2020) Jasper Fuk-Woo Chan et al.   LANCET

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

(2020) Qun Li et al.   NEW ENGLAND JOURNAL OF MEDICINE

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens

(2018) Sergei L Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission

(2018) Doreen Muth et al.   Scientific Reports

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

(2016) Shuo Su et al.   TRENDS IN MICROBIOLOGY

Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus

(2014) M. Cotten et al.   mBio

Middle East Respiratory Syndrome Coronavirus (MERS-CoV): Announcement of the Coronavirus Study Group

(2013) R. J. de Groot et al.   JOURNAL OF VIROLOGY

Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study

(2013) Matthew Cotten et al.   LANCET

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

(2012) Ali M. Zaki et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ecoepidemiology and Complete Genome Comparison of Different Strains of Severe Acute Respiratory Syndrome-Related Rhinolophus Bat Coronavirus in China Reveal Bats as a Reservoir for Acute, Self-Limiting Infection That Allows Recombination Events

(2010) S. K. P. Lau et al.   JOURNAL OF VIROLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Many-core algorithms for statistical phylogenetics

(2009) M. A. Suchard et al.   BIOINFORMATICS