About WebCVTree

WebCVTree is a web-based platform for studying phylogeny and taxonomy of prokaryotes. WebCVTree was first developed in 2004 by Professor Bailin Hao and colleagues. Using WebCVTree, users can build phylogenetic trees based on whole-genome data by using CVTree algorithm, study species evolution based on the phylogenetic trees, and investigate taxonomic systems based on evolution; if users have genomes of unknown strains, they can also infer their lineage based on current taxonomic systems.

In WebCVTree4, the redesigned CVTree (Composition Vector Tree) program can better utilize caching, thereby making better use of the intermediate data results cached in the built-in database to improve the speed of constructing phylogenetic trees from gene sequences. At the same time, the newly designed CLTree (Collapse Lineage Tree) algorithm can efficiently compare the generated phylogenetic relationships with the taxonomic system, thereby facilitating the study of species evolution and taxonomy based on gene sequences. Additionally, it is based on HTML5 technology to enable the display, interaction, and saving of phylogenetic trees. Here are key technologies of WebCVTree4:

• CVTree: CVTree is the core algorithm of WebCVTree4. It was proposed by Professor Bailin Hao and colleagues in 2004. It is an implementation of alignment-free algorithms for generating dissimilarity matrices from large collections of DNA or amino acid sequences, preferably genome data, for phylogenetic studies. It was first developed to infer evolutionary relatedness of microbial organisms and then successfully applied to viruses, chloroplasts, and fungi.
• Built-in Data: WebCVTree4 is based on NCBI’s RefSeq database, integrating hundreds of thousands of prokaryotic genomes, and utilizes the CVTree program’s caching mechanism to retain a large number of intermediate results, thereby accelerating the construction of phylogenetic trees.
• CLTree：CLTree is an algorithm that compares the phylogenetic tree with a taxonomic system. It annotates the phylogenetic tree with taxonomic information. Furthermore, based on this taxonomic information, CLTree determines a suitable root for the unrooted tree.
• Visualization: WebCVTree4 provides a web-based visualization interface, allowing users to view and interact with phylogenetic trees directly in the browser, and export high-quality phylogenetic tree images.

Statistics of Built-in Data

References

• Zuo, G (2026). WebCVTree4: A Novel Phylogenetic and Taxonomic Study Platform for Prokaryotes Using Composition Vectors and Whole Genomes. In Submission.
• Zuo, G (2025). CLTree: Annotating, Rooting, and Evaluating Phylogenetic Trees Based on Genome Lineages. arXiv:2511.17996
• Zuo, G (2021). CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes. Genomics Proteomics & Bioinformatics, 19, 662-667.
• Zuo G, Hao B (2015). CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics, 13, 321–331.
• Xu Z, Hao B (2009). CVTree update: A newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res, 37, W174-178.
• Qi J, Luo H, Hao B (2004). CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res, 32, W45-47.
• Qi, J., Wang, B., Hao, B. (2004). Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. Journal of Molecular Evolution, 58, 1-11.

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