Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Abstract

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.

Figure 1.

iTOL’s user interface. Phylogenetic tree annotated with a multi-value bar chart is displayed, with the interactive dataset editor open. Data is entered through a spreadsheet-like interface. Tree nodes can be easily selected with an autocomplete search interface. Clicking the nodes in the editor zooms and pans the tree to show their exact location. Dataset legends and scales can be similarly edited.

Figure 2.

New dataset types in iTOL v4. Each tree in iTOL can be annotated with an unlimited number of datasets. Dataset files are drag-dropped onto the trees displayed in the browser and visualized automatically. (A) Images: External bitmap and SVG images can be linked to any tree node, any individually scaled, rotated and positioned. (B) Multiple sequence alignments: Raw FASTA multiple sequence alignments are supported. Several standard color schemes are available, and custom colors can be defined for each residue. Consensus sequence and the residue conservation graph are calculated automatically. (C) Branch and label styles: colors and styles for tree nodes and labels can now be specified through a separate dataset type. There can be multiple different styles datasets present, allowing users to simply switch between various tree colors and styles. (D) Line charts: Visualized as a series of points, optionally connected with a line. Vertical and horizontal axis lines are supported, as well as automatic coloring of the dots/lines based on user specified value thresholds. Vertical and horizontal display styles are available, both on rectangular and circular trees.