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

Bioinformatics. 2015 Sep 1;31(17):2877-8. doi: 10.1093/bioinformatics/btv271. Epub 2015 Apr 25.


We announce the release of kSNP3.0, a program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. kSNP3.0 is a significantly improved version of kSNP v2.

Availability and implementation: kSNP3.0 is implemented as a package of stand-alone executables for Linux and Mac OS X under the open-source BSD license. The executable packages, source code and a full User Guide are freely available at https://sourceforge.net/projects/ksnp/files/

Contact: barryghall@gmail.com.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Databases, Nucleic Acid
  • Escherichia coli / classification
  • Escherichia coli / genetics*
  • Genome, Bacterial*
  • Molecular Sequence Annotation
  • Phylogeny*
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA / methods*
  • Software*