Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees

Abstract

Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new ‘Demo’ trees to demonstrate the basic functionalities of Evolview, and five new ‘Showcase’ trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/.

Golgi‐localized cation/proton exchangers regulate ionic homeostasis and skotomorphogenesis in Arabidopsis

“…Bootstrap values of 1,000 replicates are shown on each branch point of the tree. The tree was customized and annotated with an online visualization and management tool, Evolview (He et al, ).…”

Alterations of c‐di‐GMP turnover proteins modulate semi‐constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli

“…Alignment of the concatenated 2353 core genes was done with MAFFT (Katoh & Standley, ) and the tree was computed with FastTree (Price, Dehal, & Arkin, ). Evolview (He et al., ) was applied for the tree layout. MLST typing was done online using the service provided by the Center for Genomic Epidemiology, Technical University of Denmark, at https://cge.cbs.dtu.dk/services/MLST/#ref04 (Larsen et al., ).…”

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

“…Phylograms may, however, be problematic for the presentation of large numbers of genotypes because Dendroscope (Huson and Scornavacca 2012)) from large datasets were also difficult to interpret. Still other graphical user interfaces were unable to even depict this large number of items, including PHYLOViZ 2.0 (Nascimento et al 2017), SplitsTree4 (Huson and Bryant 2006), EvolView (He et al 2016), Microreact (Argimon et al 2016), TreeDyn (Chevenet et al 2006),TreeView (Page 1996 and Phandango (Hadfield et al 2018).…”