Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

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. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Figure 1.

iTOL's user interface. Tree of life (12) annotated with various data sets is shown. Several branches are collapsed and displayed as triangles. Tree branches are colored according to the clade bootstrap value. Popup windows provide detailed information on clades/leaves, such as bootstrap values, taxonomical categories or associated data set values. Alternatively, popup windows can display user defined, HTML formatted text, including external links and images.

Figure 2.

Data set types supported by iTOL. Each tree in iTOL can be annotated with up to 10 different data sets. All data sets are uploaded as numeric and/or color values associated with tree nodes. (a) Binary: binary data associated with leaves. (b) Color strip and gradient: color gradients are automatically calculated from numeric data, while color strips allow direct definition of colors. (c) Bar chart and time series: set of single values associated with leaf nodes displayed as a bar chart; multiple single bar charts can be combined into an animated time series data set. (d) Stacked bar chart: a stacked set of bar charts. (e) Aligned multi value bar chart: multiple aligned bar charts. (f) Boxplot: boxplots can be uploaded as pre-calculated five-number summaries or as raw data. (g) Protein domain architecture: numerous protein domain architectures can be easily defined using 13 different geometric shapes. (h) Heatmap: colors of the map are calculated from numerical data and user defined colors gradients. (i) Pie chart: different-sized pie charts can be displayed on any node in the tree. (j) Connections: any two nodes in the tree can be connected by lines of user defined colors, widths and transparency.