Building Phylogenetic Trees From Genome Sequences With kSNP4.
SNPs
kSNP4
sequences
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
03 Nov 2023
03 Nov 2023
Historique:
received:
29
07
2023
revised:
15
10
2023
accepted:
18
10
2023
medline:
13
11
2023
pubmed:
10
11
2023
entrez:
10
11
2023
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 37948764
pii: 7390727
doi: 10.1093/molbev/msad235
pmc: PMC10640685
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
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