title: ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.
abstract: The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany huerta@embl.de.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.affiliation: Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Universitat Pompeu Fabra (UPF), 08028 Barcelona, Spain.
authors.forename: François
authors.initials: F
authors.lastname: Serra
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D023281:Genomics; D020407:Internet; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D012984:Software
keywords: NCBI taxonomy; hypothesis testing; phylogenetics.; phylogenomics; tree comparison; tree visualization