LVTree Viewer： An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics

• Published in: Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2016-04, Vol.14 (2), p.94-102
• Main Authors: Zuo, Guanghong, Zhi, Xiaoyang, Xu, Zhao, Hao, Bailin
• Format: Article
• Language: English
• Subjects: 16S rRNA phylogeny; Application Note; Archaea and Bacteria; Collapsing and expanding a tree; Firmicutes; Lineage modifications; Monophyly; Proteobacteria; rRNA基因序列; rRNA序列; 交互式; 分类单元; 原核系统; 显示; 物种树; 系统发育
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/j.gpb.2015.12.002

We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.