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

Also Consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

1. 1When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes2013 · 261 citations
2. 2Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae2012 · 80 citations
3. 3SNP-Associations and Phenotype Predictions from Hundreds of Microbial Genomes without Genome Alignments2014 · 31 citations
4. 4Distinguishing highly-related outbreak-associated Clostridium botulinum type A(B) strains2014 · 27 citations
5. 5Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads2014 · 537 citations