Doctor En Ciencias

Bioinformatics Advance Access published October 18, 2006

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
Associate Editor: Joaquin Dopazo

ABSTRACT Summary: Interactive Tree Of Life (iTOL) is a web based tool for the display, manipulation and annotation ofphylogenetic 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 Contact: bork@embl.de

Several functions are available which allow users to customize their treedisplays 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).

1

INTRODUCTION

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 stateof-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 andEddy, 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 treeswith 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).

2.1

Pruning and collapsing branches

Pruning is a process of selecting one or several branches from theoriginal 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.

2.2

Displaying external data on a tree

iTOL candisplay 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 horizontalgene 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.

2

FEATURES

2.3

Exporting trees to other formats...