Tree of Life () 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.

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 () created by EPA () or pplacer (). Placements can be visualized individually or as clade summaries, and queried through an integrated search engine.