SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

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 new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

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

(2020) Jing Lu et al.   CELL

An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

(2020) LaRinda A. Holland et al.   JOURNAL OF VIROLOGY

Spread of SARS-CoV-2 in the Icelandic Population

(2020) Daniel F. Gudbjartsson et al.   NEW ENGLAND JOURNAL OF MEDICINE

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences

(2020) Yue Xing et al.   Frontiers in Microbiology

Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay

(2020) Daniel Goldenberger et al.   JOURNAL OF VIROLOGICAL METHODS

Tracking the COVID-19 pandemic in Australia using genomics

(2020) Torsten Seemann et al.   Nature Communications

A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates

(2020) Sofia Banu et al.   Open Forum Infectious Diseases

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

(2020) Lucy van Dorp et al.   Nature Communications

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease

(2018) Bart Versteeg et al.   BMC GENOMICS

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules

(2016) Jeremiah Wala et al.   BIOINFORMATICS

Estimating diversity and entropy profiles via discovery rates of new species

(2015) Anne Chao et al.   Methods in Ecology and Evolution

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

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

Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species

(2013) Anne Chao et al.   Methods in Ecology and Evolution

Proposing a resolution to debates on diversity partitioning

(2012) Anne Chao et al.   ECOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Interplay of recombination and selection in the genomes of Chlamydia trachomatis

(2011) Sandeep J Joseph et al.   Biology Direct

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION