The emergence of SARS-CoV-2 in Europe and North America

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

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

First Case of 2019 Novel Coronavirus in the United States

(2020) Michelle L. Holshue et al.   NEW ENGLAND JOURNAL OF MEDICINE

Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany

(2020) Camilla Rothe et al.   NEW ENGLAND JOURNAL OF MEDICINE

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

(2020) Joseph R. Fauver et al.   CELL

Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series

(2020) Merle M Böhmer et al.   LANCET INFECTIOUS DISEASES

Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform

(2020) Helen Y. Chu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phylogenetic network analysis of SARS-CoV-2 genomes

(2020) Peter Forster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introductions and early spread of SARS-CoV-2 in the New York City area

(2020) Ana S. Gonzalez-Reiche et al.   SCIENCE

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

(2020) Xianding Deng et al.   SCIENCE

Cryptic transmission of SARS-CoV-2 in Washington state

(2020) Trevor Bedford et al.   SCIENCE

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences

(2018) Niema Moshiri et al.   BIOINFORMATICS

Epidemiology: Molecular mapping of Zika spread

(2017) Michael Worobey   NATURE

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

(2015) Stephanie J. Spielman et al.   PLoS One

Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography

(2014) Filip Bielejec et al.   SYSTEMATIC BIOLOGY

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

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

Fast, accurate and simulation-free stochastic mapping

(2008) V. N Minin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases

(2008) Joël Mossong et al.   PLOS MEDICINE