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BioCodeKb - Bioinformatics Knowledgebase

Phylogenetic trees are important tools in a wide variety of biological and other scientific fields, also serving as contextualization for various data types.

iTOL is an online tool, accessible with any modern web browser. The tree display engine is implemented in pure Javascript and uses the HTML5 Canvas element for visualization.

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.

There are three major groups of tree annotations in iTOL:

  • Direct interactive annotations of colors and styles for individual nodes and text labels

  • Automatic annotations based on intrinsic node features (bootstrap values, branch lengths)

  • User provided annotations associated with different nodes (datasets and other information)

iTOL provides most common functions available in any phylogenetic tree viewer. In addition to standard display formats (rectangular, circular and unrooted), iTOL supports the slanted phylogram display mode. Trees can be manipulated in various ways, and basic editing functions allow users to interactively delete or move single nodes or whole clades. Clades can also be pruned or collapsed, either manually or automatically, based on various parameters (such as associated bootstrap values or average branch length distances). Trees can be re-rooted manually on any node, or automatically using the midpoint rooting method. Tree leaves can be sorted in various ways, either manually or automatically.

iTOL supports individual style and colors for each individual node and label in the tree.

Branch support values can be visualized as various shapes with adjustable colors and sizes or as text labels. Trees with branch length information can have an internal scale with adjustable levels and colors, allowing easy estimation of distances between various clades.

The current version greatly expands the support for different fonts and font styles, with full UTF-8 character set support throughout the user interface, and the ability to use any font from the Google Web Fonts list. In addition, background color of any text label can be changed independently now.

If we are logged into our iTOL account, we can use the upload button at the bottom of each project box. We can also simply drag and drop one or multiple tree files onto the footer of each project box. Our trees should be in plain text files, and in one of the supported formats (Newick, Nexus, PhyloXML or Jplace). We can create unlimited workspaces and projects, and organize your trees using simple drag and drop. Mark projects as 'shared' to give other users access to your trees.

iTOL can easily visualize trees with 50'000 or more leaves. With advanced search capabilities and display of unrooted, circular and regular cladograms or phylograms, exploring and navigating trees of any size is simple.


Need to learn more about iTOL and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

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