ETE: a python Environment for Tree Exploration

By Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón. BMC Bioinformatics, 2010

396 citations recorded by the source corpus.

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.

Subfields: Computer Vision and Pattern Recognition, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d46fdb88fac50cd279c5cb8fbfc5aa85470cc5d6

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Citations in the corpus

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes (2015, methodology): “More specific tree processing libraries such as DendroPy [68], ETE [69], and APE [70] provide more sophisticated tools such as visualisation and tree comparison algorithms.”
A general species delimitation method with applications to phylogenetic placements (2013, methodology): “The PTP method and the pipeline are implemented in Python and rely on the python Environment for Tree Exploration package (Huerta-Cepas et al. , 2010) for tree manipulation and visualization.”
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees (2016, methodology): “(5) A canvas that shows the visualization results.”
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016, methodology): “Since its first release (Huerta-Cepas et al. 2010), ETE has been widely used as a computational framework to perform numerous phylogenomic analyses, including characterizing newly sequenced genomes (Richards et al. 2010; Wang et al. 2014), extracting information from large sets of phylogenetic…”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, methodology): “9 million phylogenetic trees were built using a slightly modified version of a previously described methodology (32,33).”
Visual comparison for information visualization (2011, neutral): “Information Visualization 2011) 17(12).”
Compact graphical representation of phylogenetic data and metadata with GraPhlAn (2015, methodology): “Among recently developed tools, iTOL ( Letunic & Bork, 2007 ; Letunic & Bork, 2011 ) targets interactive analyses of large-scale phylogenies with a moderate amount of overlaid metadata, whereas ETE ( Huerta-Cepas, Dopazo & Gabaldon, 2010 ) is a Python programming toolkit focusing on tree exploration”
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions (2010, methodology): “0 (28) to visualize phylogenetic trees, and Jalview Lite v2.”