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Mol Biol Evol. 2016 Jun;33(6):1635-8. doi: 10.1093/molbev/msw046. Epub 2016 Feb 26.

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

Author information

1
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany huerta@embl.de.
2
Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Universitat Pompeu Fabra (UPF), 08028 Barcelona, Spain.
3
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.

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.

KEYWORDS:

NCBI taxonomy; hypothesis testing; phylogenetics.; phylogenomics; tree comparison; tree visualization

PMID:
26921390
PMCID:
PMC4868116
DOI:
10.1093/molbev/msw046
[Indexed for MEDLINE]
Free PMC Article

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