Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree
display and annotation
Ivica Letunic and Peer Bork*
EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Summary: Interactive Tree Of Life (iTOL) is a web based tool for
the display, manipulation and annotation of phylogenetic trees.
Trees can be interactively pruned and re-rooted. Various types of
data such as genome sizes or protein domain repertoires can be
mapped onto the tree. Export to several bitmap and vector graphics
formats is supported.
Availability: iTOL is available through WWW at http://itol.embl.de
The amount and diversity of species with at least partial
sequence information is rapidly increasing (Cole, et al., 2005;
Tringe, et al., 2005) and the tree of life based on completely
sequenced genomes is being constantly redrawn (e.g. (Ciccarelli, et
al., 2006)). Phylogenetic trees represent a backbone for various
other biological studies and it is therefore essential to have state-
of-the-art tools for their display, customization and interpretation.
During the years, numerous tree visualization tools, both online
and standalone, have been developed. Tools like TREEVIEW
(Page, 1996), NJPLOT (Perriere and Gouy, 1996), ATV (Zmasek
and Eddy, 2001), TaxonTree (Parr, et al., 2004) and others provide
many useful features and various ways of tree visualization.
However, with advances in research and data generation, there is a
continuous need for the incorporation of novel features. Examples
are i) visualization of mid-sized trees (100 – 2000 leafs) with
branch lengths in acceptable resolutions, ii) possibility of
annotating trees with various datasets and iii) display of horizontal
gene transfers between branches. Here we describe a new tool,
iTOL, which offers these features and incorporates a layout that
was repeatedly requested by the community after its original
publication in (Ciccarelli, et al., 2006).
iTOL’s functions provide an easy way to manipulate and create
customized graphical representations of phylogenetic trees in the
standard ‘New Hampshire’ or Newick format.
In addition to the standard tree representation, trees can be
displayed in a circular (radial) mode (Figure 1), which is
particularly useful for the visualization of mid-sized trees (up to
several thousand leaves). Circular trees can be rotated and
displayed in user defined arc sizes.
*To whom correspondence should be addressed.
Several functions are available which allow users to customize
their tree displays in various ways. Branches can be pruned or
collapsed and any node can be used to re-root the tree. Colors can
be assigned to various leaf groups, simplifying the navigation
around the tree. For trees whose leaf IDs are based on NCBI
Taxonomy (Wheeler, et al., 2006), iTOL can automatically
determine taxonomic classes of all internal nodes and assign
proper scientific names to the leafs. Internal node labels are
displayed in popup windows which appear when mouse pointer is
positioned above the corresponding node (Figure 1).
Pruning is a process of selecting one or several branches from the
original tree and creating a new, smaller tree. Sub-branches and
individual leaves can be easily added or removed.
Branches whose detailed structure is not needed can be collapsed.
Collapsed branches are displayed as triangles. Total branch lengths
to the closest and the farthest leaf are used to calculate the lengths
of the triangle’s sides.
Pruning and collapsing branches
iTOL can display several types of data directly on the tree (Figure
1). Up to five datasets can be uploaded with each tree. Datasets are
contained in plain text files with each line corresponding to one
leaf in the tree. Supported dataset types are: binary data, simple
bars and stacked bars (multiple values associated with each leaf).
iTOL is the first visualization tool which supports the display of
horizontal gene transfers (HGTs) annotated directly in the original
Newick tree file. HGT information is encoded in the IDs of tree
nodes. Therefore, in addition to standard leaf IDs, the tree must
have unique IDs assigned to all internal nodes. Detailed
explanation with example trees and datasets is available in the
iTOL online help pages.
Displaying external data on a tree
Each tree display in iTOL (either default or customized) can be
exported to several graphical formats, both bitmap and vector
based. Currently supported formats are Scalable Vector Graphics
(svg), Portable Network Graphics (png), Encapsulated Postscript
(eps), Postscript (ps) and Portable Document Format (pdf). In
addition, pruned trees can be exported as Newick plain text files.
Exporting trees to other formats
Associate Editor: Joaquin Dopazo
© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: email@example.com
Bioinformatics Advance Access published October 18, 2006
by guest on June 8, 2013
Letunic and Bork
iTOL is a WWW based tool, accessible using any modern web
object which displays the tree and provides interactivity is created
dynamically by the server using a set of Perl scripts and the Ming
library (http://ming.sourceforge.net). Flash plug-in version 7 or
higher is required for full functionality. Tree export is done
through an intermediary SVG (scalable vector graphics) file, which
is converted to other formats using the Inkscape graphics package
(http://www.inkscape.org). User uploaded trees and data are stored
locally on the server and available for at least one year after
We would like to thank Christopher Creevey, Sean Hooper and
other members of the Bork group for helpful suggestions and
Ciccarelli, F.D., et al. (2006) Toward automatic reconstruction of a highly resolved
tree of life, Science, 311, 1283-1287.
Cole, J.R., et al. (2005) The Ribosomal Database Project (RDP-II): sequences and
tools for high-throughput rRNA analysis, Nucleic Acids Res, 33, D294-296.
Page, R.D. (1996) TreeView: an application to display phylogenetic trees on personal
computers, Comput Appl Biosci, 12, 357-358.
Parr, C.S., et al. (2004) Visualizations for taxonomic and phylogenetic trees,
Bioinformatics, 20, 2997-3004.
Perriere, G. and Gouy, M. (1996) WWW-query: an on-line retrieval system for
biological sequence banks, Biochimie, 78, 364-369.
Tringe, S.G., et al. (2005) Comparative metagenomics of microbial communities,
Science, 308, 554-557.
Wheeler, D.L., et al. (2006) Database resources of the National Center for
Biotechnology Information, Nucleic Acids Res, 34, D173-180.
Zmasek, C.M. and Eddy, S.R. (2001) ATV: display and manipulation of annotated
phylogenetic trees, Bioinformatics, 17, 383-384.
Fig. 1. iTOL’s user interface and example trees. The interface with a tree of life (Ciccarelli, et al., 2006), annotated with genome sizes (blue bars), is
shown. Several branches are collapsed and displayed as triangles. Popup windows give detailed information on branches/leaves, such as bootstrap
values and taxonomical categories. a) A 200 species tree displayed in a 180° arc with a stacked bar dataset. b) A protein kinases tree displayed without
branch length information and annotated with predicted site counts for various families.
by guest on June 8, 2013