Building Phylogenetic Trees From Genome Sequences With kSNP4.

Area of Science:

• Genomics and Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Phylogenetic analysis using whole genome sequences provides maximal information for resolving evolutionary relationships.
• Single-nucleotide polymorphisms (SNPs) offer a powerful approach for phylogenetic inference, especially with large datasets like hundreds of microbial genomes, and bypass the need for genome alignments.

Purpose of the Study:

• To introduce and provide a detailed protocol for kSNP4, a novel software tool for phylogenetic analysis.
• To demonstrate the utility of kSNP4 in identifying SNPs and constructing phylogenetic trees from genome sequences without a reference genome.

Main Methods:

• kSNP4 identifies SNPs directly from genome sequences, obviating the need for a reference genome or multiple sequence alignments.
• The software implements parsimony, maximum likelihood, and neighbor-joining methods for phylogenetic tree estimation.
• kSNP4 includes functionality for annotating identified SNPs and is a self-contained, command-line program.

Main Results:

• kSNP4 successfully identifies SNPs and constructs phylogenetic trees from genome sequences.
• The program is designed for ease of use, requiring no prior programming or bioinformatics expertise.
• A comprehensive user guide is provided, detailing installation and all features of kSNP4.

Conclusions:

• kSNP4 is an accessible and efficient tool for microbial phylogenetic analysis using genome-wide SNPs.
• The software democratizes advanced phylogenetic methods, making them available to a broad range of users from students to senior researchers.
• This protocol facilitates the adoption and application of kSNP4 for robust evolutionary studies.