kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome: Table 1

Distinguishing highly-related outbreak-associated Clostridium botulinum type A(B) strains

(2014) Brian H Raphael et al.   BMC MICROBIOLOGY

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

SNP-Associations and Phenotype Predictions from Hundreds of Microbial Genomes without Genome Alignments

(2014) Barry G. Hall   PLoS One

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

(2014) Brian M. Forde et al.   PLoS One

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

(2013) Shea N. Gardner et al.   PLoS One

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

(2012) Brendan Epstein et al.   PLoS Genetics