Abstract
BackgroundMany bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale.ResultsHere we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations.ConclusionsETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.
Highlights
Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result
For instance, trees are used to illustrate the evolutionary relationships among species or molecular sequences, considering terminal nodes as extant Operational Taxonomic Units (OTU) and internal nodes as their corresponding ancestors
An intermediate alternative between standalone viewers and programmatic tree rendering is that of the TreeDyn program [14], which has support for some scripting options and can be used to create fully annotated tree images. In response to these limitations, we present here the Environment for Tree Exploration (ETE), a python programming toolkit to analyze, manipulate or visualize any kind of hierarchical tree
Summary
Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result These are used to represent the relationships among different biological entities, facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them Such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. When the analysis of hundreds or thousands of trees is required, the use of standalone programs becomes restrictive, because a much higher level of automation is required In such cases, programming toolkits represent a more adequate framework, since they provide tools and methods to handle data at a lower level. An intermediate alternative between standalone viewers and programmatic tree rendering is that of the TreeDyn program [14], which has support for some scripting options and can be used to create fully annotated tree images
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