Separation and assembly of deep sequencing data into discrete sub-population genomes

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: Modeling studies of antibody and receptor binding

(2015) Abhisek Kumar Behera et al.   GENE

Single Genome Analysis for the Detection of Linked Multiclass Drug Resistance Mutations in HIV-1-Infected Children After Failure of Protease Inhibitor-Based First-Line Therapy

(2015) Camille Marie Lange et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Advanced Molecular Surveillance of Hepatitis C Virus

(2015) Livia Rossi et al.   Viruses-Basel

Accurate viral population assembly from ultra-deep sequencing data

(2014) S. Mangul et al.   BIOINFORMATICS

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis

(2014) Luis Santana-Quintero et al.   PLoS One

Viral Quasispecies Assembly via Maximal Clique Enumeration

(2014) Armin Töpfer et al.   PLoS Computational Biology

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

When to start antiretroviral therapy: the need for an evidence base during early HIV infection

(2013) Jens D Lundgren et al.   BMC Medicine

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

(2013) Sandhya Prabhakaran et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges

(2013) Mattia C. F. Prosperi et al.   Scientific Reports

De novo assembly of highly diverse viral populations

(2012) Xiao Yang et al.   BMC GENOMICS

Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes

(2012) M. Schirmer et al.   BRIEFINGS IN BIOINFORMATICS

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

(2012) Osvaldo Zagordi et al.   PLoS One

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing

(2011) Mattia CF Prosperi et al.   BMC BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Ultra-deep sequencing for the analysis of viral populations

(2011) Niko Beerenwinkel et al.   Current Opinion in Virology

The RNA Virus Quasispecies: Fact or Fiction?

(2010) Edward C. Holmes   JOURNAL OF MOLECULAR BIOLOGY

Viral Mutation Rates

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

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology

(2010) Stephanie M. Willerth et al.   PLoS One

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology