Bellingham Research Institute, Portland, OR, USA.
Mol Biol Evol. 2023 Nov 3;40(11). doi: 10.1093/molbev/msad235.
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.
使用基因组序列进行系统发育分析可以最大限度地利用信息来估计系统发育和密切相关分类群的分辨率。使用单核苷酸多态性 (SNP) 可以在不进行基因组比对的情况下估计系统发育树，并可以使用数百个微生物基因组的数据集。kSNP4 是一种无需参考基因组即可识别 SNP 的程序，它可以估计简约法、最大似然法和邻接法树，并能够注释发现的 SNP。kSNP4 是一个命令行程序，无需安装或使用任何其他程序或依赖项。kSNP4 无需任何编程经验或生物信息学经验即可安装和使用。它适合学生和高级研究人员使用。它包含一个详细的用户指南，其中解释了 kSNP4 的所有许多功能。在这项研究中，我们提供了一个详细的逐步协议，用于下载、安装和使用 kSNP4 从基因组序列构建系统发育树。
