Composition Vector Tree (CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16S rRNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.

组合向量树 ( CVTree ) 是一种无需比对的算法，用于从基因组序列推断系统发育关系。它已成功应用于系统发育和分类学研究基于全基因组的病毒、原核生物和真菌，以及叶绿体基因组、线粒体基因组和宏基因组。在这里，我们介绍了 CVTree 算法的独立软件。在软件中，为CVTree算法设计了一个可扩展的并行工作流程。基于工作流程，还实施了新的无对齐方法。通过基于 16S rRNA 序列检查 13,903 种原核生物的系统发育和分类，我们发现 CVTree 软件是基于基因组序列研究系统发育和分类的有效工具。CVTree 软件的代码可以在 https://github.com/ghzuo/cvtree 获得。