Building Phylogenetic Trees from Genome Sequences with kSNP4

Bellingham Research Institute Director Barry G. Hall and Senior Scientist Jeremiah Nisbet have just published a paper entitled “Building phylogenetic trees from genome sequences with kSNP4” in the journal Molecular Biology and Evolution (Mol. Biol. Evol. 40  ) The paper is freely available by clicking the link.

Performing phylogenetic analysis with genome sequences maximizes the information used to estimate phylogenies and maximizes the resolution of closely related taxa. The use of SNPs (single-nucleotide polymorphisms) permits estimating trees without genome alignments and permits the use of datasets of hundreds of microbial genomes. kSNP4 is a program that identifies SNPs without using a reference genome, estimates Parsimony, Maximum Likelihood, and Neighbor Joining trees and is able to annotate the discovered SNPs.

kSNP4 is a command-line program that does not require any additional programs or dependencies to install or use. kSNP4 does not require any programming experience or bioinformatics experience to install and use. It is suitable for use by students through senior investigators. It includes a detailed User Guide that explains all of the features of kSNP4.

Here we provide a detailed step-by-step protocol for downloading, installing and using kSNP4 to build phylogenetic trees from genome sequences.

The current version, kSNP 4.1, is freely available for Mac OS and Linux platforms from and includes complete documentation.

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