ArticleMolecular biology and evolution2023
Building Phylogenetic Trees From Genome Sequences With kSNP4.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- A Simplified Guide to Whole-Genome Sequence Analysis of Salmonella on the Command Line.Methods in molecular biology (Clifton, N.J.) · 2027Article
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- Clinical and molecular characteristics of Streptococcus agalactiae bacteremia in nonpregnant adults: a single-center analysis over 16 years in Hiroshima, Japan.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Genetic engineering ofMicrobial genomics · 2026Article
- Phylogenetic analysis of serotype 19A-sequence type (ST)2331Microbial genomics · 2026Article
- Genomic characterization of invasiveMicrobial genomics · 2026Article
- Probing Genomic Diversity ofFoods (Basel, Switzerland) · 2026Article
- Genome on the move: emergence of hybrid atypical enteropathogenic/enteroaggregativeMicrobiology spectrum · 2026Article
- Comparative Genomics Reveals Unique Genetic Determinants of Biofilm Formation inInternational journal of molecular sciences · 2026Article
- Integrating ANI and phylogenies for re-evaluation of Fusobacterium taxonomy and disease associations.Nature communications · 2026Article
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- Phylogeographic clustering ofApplied and environmental microbiology · 2026Article
- Emergence of NDM-type metallo-β-lactamase and ArmA 16S rRNA methylase co-producing Morganella morganii in Myanmar.BMC infectious diseases · 2026Article
- Plasmidomic landscape of Staphylococcus aureus and the emergence of a CC5 subclade harboring the conjugative plasmid pSK41: implications for food safety and antimicrobial resistance.NPJ science of food · 2026Article
- Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems.The ISME journal · 2026Article
- BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.Nucleic acids research · 2026Article
- Genomic and epidemiologic evidence for attenuated virulence inFrontiers in microbiology · 2026Article
- Comparative phylogenetic, antimicrobial resistance, and clinical characterization of human spondylodiscitis-associatedFrontiers in microbiology · 2026Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Performing phylogenetic analysis with genome sequences maximizes the information used to estimate phylogenies and the resolution of closely related taxa. The use of single-nucleotide polymorphisms (SNPs) permits estimating trees without genome alignments and permits the use of data sets 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 many features of kSNP4. In this study, we provide a detailed step-by-step protocol for downloading, installing, and using kSNP4 to build phylogenetic trees from genome sequences.
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