Finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation. kSNP3 now available.
Biology, Genetics, Molecular genetics, Genetic variation, DNA polymorphism
Gardner SN, Hall BG "When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes." PLoS ONE 2013; 8(12):e81760 https://doi.org/10.1371/journal.pone.0081760
Gardner SN, Slezak T, Hall BG "kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome." Bioinformatics 2015; 31(17):2877-8 https://doi.org/10.1093/bioinformatics/btv271
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