Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Abstract

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.

Figure 1.

Tree of Life (15) annotated with various datasets, highlighting several novel features, along with iTOL's interactive user interface. Tree branches are colored and displayed with varying styles and widths. Support values are visualized as triangles of varying size. An internal tree scale is displayed, with user-defined colors and level values. A text label dataset was precisely positioned above the colored strips using interactive controls. Several dataset types can include user-defined scales.

Figure 2.

New and significantly changed dataset types in iTOL version 3. 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) Binary: multiple columns are now supported, with different colors and shapes. (B) Symbols: Various shapes of user-defined size and color can be displayed anywhere along tree branches. (C) Connections: supported in any tree display mode, they are visualized as straight or curved links between any two nodes, with or without arrows heads. (D) Text labels: any text of individually adjustable size, color, style, and rotation angle can be positioned anywhere along branches, or on the outside of the tree. (E) Shape plots: multiple values associated with nodes are displayed as geometric shapes of different sizes in consecutive columns outside the tree, optionally with value labels. (F) Heatmap: an additional tree can be displayed above the heatmap, and will be used to automatically sort the data columns. (G) External pie charts: pie charts can now also be displayed outside the tree, with adjustable sizes and positions. (H) Phylogenetic placements: generated automatically from user uploaded .jplace files (11) created by EPA (12) or pplacer (13). Placements can be visualized individually or as clade summaries, and queried through an integrated search engine.