Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

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

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

(2020) Jing Lu et al.   CELL

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

(2020) Joseph R. Fauver et al.   CELL

Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe

(2020) Paola Stefanelli et al.   Eurosurveillance

Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes

(2020) Peter Ralph et al.   GENETICS

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

(2020) Tommy Tsan-Yuk Lam et al.   NATURE

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

Introductions and early spread of SARS-CoV-2 in France, 24 January to 23 March 2020

(2020) Fabiana Gámbaro et al.   Eurosurveillance

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

(2020) Rebecca J. Rockett et al.   NATURE MEDICINE

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

(2020) Xianding Deng et al.   SCIENCE

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region

(2020) Matthew T Maurano et al.   GENOME RESEARCH

The UCSC SARS-CoV-2 Genome Browser

(2020) Jason D. Fernandes et al.   NATURE GENETICS

Cryptic transmission of SARS-CoV-2 in Washington state

(2020) Trevor Bedford et al.   SCIENCE

An Evolving View of Phylogenetic Support

(2020) Chris Simon   SYSTEMATIC BIOLOGY

Phylogenetic analysis of SARS-CoV-2 data is difficult

(2020) Benoit Morel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka

(2020) Chitra Pattabiraman et al.   PLoS One

Stability of SARS-CoV-2 phylogenies

(2020) Yatish Turakhia et al.   PLoS Genetics

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

(2018) Pierre Barbera et al.   SYSTEMATIC BIOLOGY

Efficient pedigree recording for fast population genetics simulation

(2018) Jerome Kelleher et al.   PLoS Computational Biology

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

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

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh 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

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

TreeCmp: Comparison of Trees in Polynomial Time

(2012) Damian Bogdanowicz et al.   Evolutionary Bioinformatics

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One