Stability of SARS-CoV-2 phylogenies

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 Genomic Perspective on the Origin and Emergence of SARS-CoV-2

(2020) Yong-Zhen Zhang et al.   CELL

Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)

(2020) A. Bal et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

(2020) Timothy M. Freeman et al.   GENOME RESEARCH

Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy

(2020) Gianguglielmo Zehender et al.   JOURNAL OF MEDICAL VIROLOGY

The establishment of reference sequence for SARS‐CoV‐2 and variation analysis

(2020) Changtai Wang et al.   JOURNAL OF MEDICAL VIROLOGY

Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant

(2020) Maria Pachetti et al.   Journal of Translational Medicine

Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

(2020) P. Simmonds   mSphere

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

(2020) Lucy van Dorp et al.   INFECTION GENETICS AND EVOLUTION

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Tracking virus outbreaks in the twenty-first century

(2018) Nathan D. Grubaugh et al.   Nature Microbiology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

Error baseline rates of five sample preparation methods used to characterize RNA virus populations

(2017) Jeffrey R. Kugelman et al.   PLoS One

nextflu: real-time tracking of seasonal influenza virus evolution in humans

(2015) Richard A. Neher et al.   BIOINFORMATICS

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

(2015) Richard J Orton et al.   BMC GENOMICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY