When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

Bioinformatics for microbial genotyping of equine encephalitis viruses, orthopoxviruses, and hantaviruses

(2013) Shea N. Gardner et al.   JOURNAL OF VIROLOGICAL METHODS

Using Complete Genome Comparisons to Identify Sequences Whose Presence Accurately Predicts Clinically Important Phenotypes

(2013) Barry G. Hall et al.   PLoS One

Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments

(2012) David A. Hysom et al.   PLoS One

Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination

(2012) Weilong Hao et al.   PLoS One

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

(2012) Sanaa A. Ahmed et al.   PLoS One

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Inadequacies of Minimum Spanning Trees in Molecular Epidemiology

(2011) S. J. Salipante et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

(2009) Bryan Kolaczkowski et al.   PLoS One

Simulating DNA Coding Sequence Evolution with EvolveAGene 3

(2008) B. G. Hall   MOLECULAR BIOLOGY AND EVOLUTION