CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

Xu, Zhao; Hao, Bailin

Users get to the tree page by following the 'Show collapsed trees' link in the result page. In this page, we provide trees partially 'collapsed' to certain taxonomic level according to the NCBI taxonomy. The necessity of so doing requires some explanation. At present, the progress of prokaryotic and fungal phylogeny has made detailed comparison with taxonomy feasible. However, it is not easy to comprehend a tree with hundreds or more leaves. To simplify the job, we collapse an original genome tree to different taxonomic levels taking monophyleticity of branches as a guiding principle. For example, at the phylum level the 36 species/strains classified as Cyanobacteria do form a monophyletic branch. This branch is replaced by a single node labeled by Cyanobacteriaf36g. The reduction can only be partial, as, for example, the phylum Proteobacteria does not appear as a monophyletic group in a tree. However, three out of the five classes in this phylum do form monophyletic branches. Therefore, Alphaproteobacteriaf104g, Betaproteobacteriaf62g and Epsilonproteobacteriaf24g nodes appear when the tree is collapsed to class level. In this way, the number of leaves in a collapsed tree may be greatly reduced.